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Volume 66(Pt 10);  2010 October 1

JCSG pipeline: technology and dissemination

Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, John Wooley, Kurt Wüthrich, Ian A. Wilson

The Joint Center for Structural Genomics high-throughput structural biology pipeline has delivered more than 1000 structures to the community over the past ten years and has made a significant contribution to the overall goal of the NIH Protein Structure Initiative (PSI) of expanding structural coverage of the protein universe.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1137–1142. Published online 2010 September 30. doi: 10.1107/S1744309110038212
PMCID:
PMC2954196
S. Sri Krishna, Dana Weekes, Constantina Bakolitsa, Marc-André Elsliger, Ian A. Wilson, Adam Godzik, John Wooley

Specific use cases of TOPSAN, an innovative collaborative platform for creating, sharing and distributing annotations and insights about protein structures, such as those determined by high-throughput structural genomics in the Protein Structure Initiative (PSI), are described. TOPSAN is the main annotation platform for JCSG structures and serves as a conduit for initiating collaborations with the

...
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1143–1147. Published online 2010 September 30. doi: 10.1107/S1744309110035736
PMCID:
PMC2954197

Domains of Unknown Function

Alex Bateman, Penny Coggill, Robert D. Finn

Domains of unknown function (DUFs) are a large set of uncharacterized protein families that structural genomics is helping biologists to understand functionally.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1148–1152. Published online 2010 March 5. doi: 10.1107/S1744309110001685
PMCID:
PMC2954198
Hsiu-Ju Chiu, Constantina Bakolitsa, Arne Skerra, Andrei Lomize, Dennis Carlton, Mitchell D. Miller, S. Sri Krishna, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Thomas Clayton, Marc C. Deller, Lian Duan, Julie Feuerhelm, Joanna C. Grant, Slawomir K. Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, Abhinav Kumar, David Marciano, Daniel McMullan, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Jessica Paulsen, Ron Reyes, Christopher L. Rife, Henry van den Bedem, Dana Weekes, Qingping Xu, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

NE1406, the first structural representative of PF09410, reveals a lipocalin-like fold with features that suggest involvement in lipid metabolism. In addition, NE1406 provides potential structural templates for two other protein families (PF07143 and PF08622).

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1153–1159. Published online 2009 December 8. doi: 10.1107/S1744309109037749
PMCID:
PMC2954199
S. Sri Krishna, L. Aravind, Constantina Bakolitsa, Jonathan Caruthers, Dennis Carlton, Mitchell D. Miller, Polat Abdubek, Tamara Astakhova, Herbert L Axelrod, Hsiu-Ju Chiu, Thomas Clayton, Marc C. Deller, Lian Duan, Julie Feuerhelm, Joanna C. Grant, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Abhinav Kumar, David Marciano, Daniel McMullan, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Ron Reyes, Christopher L. Rife, Henry van den Bedem, Dana Weekes, Qingping Xu, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structure of SSO2064, the first structural representative of Pfam family PF01796 (DUF35), reveals a two-domain architecture comprising an N-terminal zinc-ribbon domain and a C-terminal OB-fold domain. Analysis of the domain architecture, operon organization and bacterial orthologs combined with the structural features of SSO2064 suggests a role involving acyl-CoA binding for this family

...
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1160–1166. Published online 2010 March 5. doi: 10.1107/S1744309110002514
PMCID:
PMC2954200
Mitchell D. Miller, L. Aravind, Constantina Bakolitsa, Christopher L. Rife, Dennis Carlton, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Hsiu-Ju Chiu, Thomas Clayton, Marc C. Deller, Lian Duan, Julie Feuerhelm, Joanna C. Grant, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, Abhinav Kumar, David Marciano, Daniel McMullan, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Ron Reyes, Henry van den Bedem, Dana Weekes, Qingping Xu, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structure of the first representative of DUF364 family reveals a combination of enolase N-terminal-like and C-terminal Rossmann-like folds. Analysis of the interdomain cleft combined with sequence and genome context conservation among homologs, suggests a unique catalytic site likely involved in the synthesis of a flavin or pterin derivative.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1167–1173. Published online 2010 July 6. doi: 10.1107/S1744309110007517
PMCID:
PMC2954201
Debanu Das, Nick V. Grishin, Abhinav Kumar, Dennis Carlton, Constantina Bakolitsa, Mitchell D. Miller, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Prasad Burra, Connie Chen, Hsiu-Ju Chiu, Michelle Chiu, Thomas Clayton, Marc C. Deller, Lian Duan, Kyle Ellrott, Dustin Ernst, Carol L. Farr, Julie Feuerhelm, Anna Grzechnik, Slawomir K. Grzechnik, Joanna C. Grant, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Hope A. Johnson, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, David Marciano, Daniel McMullan, Andrew T. Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Silvya Oommachen, Jessica Paulsen, Christina Puckett, Ron Reyes, Christopher L. Rife, Natasha Sefcovic, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Tiffany Wooten, Qingping Xu, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structure of the NGO1945 gene product from N. gonorrhoeae (UniProt Q5F5IO) reveals that the N-terminal domain assigned as a domain of unknown function (DUF2063) is likely to bind DNA and that the protein may be involved in transcriptional regulation.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1174–1181. Published online 2009 October 27. doi: 10.1107/S1744309109022672
PMCID:
PMC2954202
Constantina Bakolitsa, Abhinav Kumar, Kevin K. Jin, Daniel McMullan, S. Sri Krishna, Mitchell D. Miller, Polat Abdubek, Claire Acosta, Tamara Astakhova, Herbert L. Axelrod, Prasad Burra, Dennis Carlton, Connie Chen, Hsiu-Ju Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Ylva Elias, Kyle Ellrott, Dustin Ernst, Carol L. Farr, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Slawomir K. Grzechnik, Gye Won Han, Lukasz Jaroszewski, Hope A. Johnson, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, David Marciano, Andrew T. Morse, Kevin D. Murphy, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Jessica Paulsen, Christina Puckett, Ron Reyes, Christopher L. Rife, Natasha Sefcovic, Henry J. Tien, Christine B. Trame, Christina V. Trout, Henry van den Bedem, Dana Weekes, Aprilfawn White, Qingping Xu, Keith O. Hodgson, John Wooley, Marc-Andre Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

Structures of the first representatives of PF06684 (DUF1185) reveal a Bacillus chorismate mutase-like fold with a potential role in amino-acid synthesis.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1182–1189. Published online 2010 March 5. doi: 10.1107/S1744309109050647
PMCID:
PMC2954203

New Folds

Antonina Andreeva, Alexey G. Murzin

This review article surveys the protein structures determined by Joint Center for Structural Genomics and published in this special issue of Acta Crystallographica Section F.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1190–1197. Published online 2010 July 6. doi: 10.1107/S1744309110007177
PMCID:
PMC2954204
Constantina Bakolitsa, Alex Bateman, Kevin K. Jin, Daniel McMullan, S. Sri Krishna, Mitchell D. Miller, Polat Abdubek, Claire Acosta, Tamara Astakhova, Herbert L. Axelrod, Prasad Burra, Dennis Carlton, Hsiu-Ju Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Ylva Elias, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Slawomir K. Grzechnik, Gye Won Han, Lukasz Jaroszewski, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, Abhinav Kumar, David Marciano, Andrew T. Morse, Kevin D. Murphy, Edward Nigoghossian, Linda Okach, Silvya Oommachen, Jessica Paulsen, Ron Reyes, Christopher L. Rife, Natasha Sefcovic, Henry Tien, Christine B. Trame, Christina V. Trout, Henry van den Bedem, Dana Weekes, Aprilfawn White, Qingping Xu, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott Lesley, Ian A. Wilson

The crystal structure of the first representative of the Pfam PF07336 (DUF1470) family reveals a two-domain organization that contains a new fold, termed the ABATE domain, at the N-terminus and a treble-clef zinc finger that is likely to bind DNA at the C-terminus.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1198–1204. Published online 2009 October 27. doi: 10.1107/S1744309109025196
PMCID:
PMC2954205
Constantina Bakolitsa, Abhinav Kumar, Dennis Carlton, Mitchell D. Miller, S. Sri Krishna, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Hsiu-Ju Chiu, Thomas Clayton, Marc C. Deller, Lian Duan, Marc-André Elsliger, Julie Feuerhelm, Slawomir K. Grzechnik, Joanna C. Grant, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, David Marciano, Daniel McMullan, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Silvya Oommachen, Jessica Paulsen, Ron Reyes, Christopher L. Rife, Henry J. Tien, Christina V. Trout, Henry van den Bedem, Dana Weekes, Qingping Xu, Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The first structural representative of the PF08866 (DUF1831) protein family reveals a potential new α+β fold and indicates a possible involvement in amino-acid metabolism.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1205–1210. Published online 2009 October 27. doi: 10.1107/S1744309109023689
PMCID:
PMC2954206
Constantina Bakolitsa, Abhinav Kumar, Daniel McMullan, S. Sri Krishna, Mitchell D. Miller, Dennis Carlton, Rafael Najmanovich, Polat Abdubek, Tamara Astakhova, Hsiu-Ju Chiu, Thomas Clayton, Marc C. Deller, Lian Duan, Ylva Elias, Julie Feuerhelm, Joanna C. Grant, Slawomir K. Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, David Marciano, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Silvya Oommachen, Jessica Paulsen, Ron Reyes, Christopher L. Rife, Christina V. Trout, Henry van den Bedem, Dana Weekes, Aprilfawn White, Qingping Xu, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

PA1994, a Pfam PF06475 (DUF1089) family homolog from P. aeruginosa, reveals remote similarities to lipoprotein localization factors and a conserved putative glycolipid-binding site.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1211–1217. Published online 2009 October 27. doi: 10.1107/S1744309109022684
PMCID:
PMC2954207
Gye Won Han, Constantina Bakolitsa, Mitchell D. Miller, Abhinav Kumar, Dennis Carlton, Rafael J. Najmanovich, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Connie Chen, Hsiu-Ju Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Dustin Ernst, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Lukasz Jaroszewski, Kevin K. Jin, Hope A. Johnson, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, David Marciano, Daniel McMullan, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Ron Reyes, Christopher L. Rife, Natasha Sefcovic, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Qingping Xu, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structures of SPO0140 and Sbal_2486 revealed a two-domain structure that adopts a novel fold. Analysis of the interdomain cleft suggests a nucleotide-based ligand with a genome context indicating signaling as a possible role for this family.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1218–1225. Published online 2010 March 5. doi: 10.1107/S1744309109050416
PMCID:
PMC2954208

Novel Variants of Known Folds and Function

Eugene V. Koonin

New distinct versions of known protein folds provide a powerful means of protein-function prediction that complements sequence and genomic context analysis.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1226–1229. Published online 2010 July 6. doi: 10.1107/S1744309110013242
PMCID:
PMC2954209
Qingping Xu, Daniel McMullan, Lukasz Jaroszewski, S. Sri Krishna, Marc-André Elsliger, Andrew P. Yeh, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Dennis Carlton, Hsiu-Ju Chiu, Thomas Clayton, Lian Duan, Julie Feuerhelm, Joanna Grant, Gye Won Han, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Mitchell D. Miller, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Silvya Oommachen, Jessica Paulsen, Ron Reyes, Christopher L. Rife, Henry van den Bedem, Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structure of an essential bacterial protein, YeaZ, from T. maritima identifies an interface that potentially mediates protein–protein interaction.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1230–1236. Published online 2009 October 27. doi: 10.1107/S1744309109022192
PMCID:
PMC2954210
Gye Won Han, Marc-André Elsliger, Todd O. Yeates, Qingping Xu, Alexey G. Murzin, S. Sri Krishna, Lukasz Jaroszewski, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Dennis Carlton, Connie Chen, Hsiu-Ju Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Dustin Ernst, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Kevin K. Jin, Hope A. Johnson, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, Abhinav Kumar, Winnie W. Lam, David Marciano, Daniel McMullan, Mitchell D. Miller, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Ron Reyes, Christopher L. Rife, Natasha Sefcovic, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structure of a putative NTP pyrophosphohydrolase, YP_001813558.1 from E. sibiricum, reveals a novel segment-swapped linked-dimer assembly.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1237–1244. Published online 2010 August 4. doi: 10.1107/S1744309110025534
PMCID:
PMC2954211
Abhinav Kumar, Andrei Lomize, Kevin K. Jin, Dennis Carlton, Mitchell D. Miller, Lukasz Jaroszewski, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Hsiu-Ju Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Gye Won Han, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, David Marciano, Daniel McMullan, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Ron Reyes, Christopher L. Rife, Natasha Sefcovic, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Qingping Xu, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structures of two orthologous proteins from different Shewanella species have uncovered a resemblance to CRAL-TRIO carrier proteins, which suggest that they function as transporters of small nonpolar molecules. One protein adopts an open conformation, while the other adopts a closed structure that may act as a conformational switch in the transport of ligands at the membrane surface.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1245–1253. Published online 2009 December 8. doi: 10.1107/S1744309109042481
PMCID:
PMC2954212
Debanu Das, Piotr Kozbial, Gye Won Han, Dennis Carlton, Lukasz Jaroszewski, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Constantina Bakolitsa, Connie Chen, Hsiu-Ju Chiu, Michelle Chiu, Thomas Clayton, Marc C. Deller, Lian Duan, Kyle Ellrott, Marc-André Elsliger, Dustin Ernst, Carol L. Farr, Julie Feuerhelm, Anna Grzechnik, Joanna C. Grant, Kevin K. Jin, Hope A. Johnson, Heath E. Klock, Mark W. Knuth, S. Sri Krishna, Abhinav Kumar, David Marciano, Daniel McMullan, Mitchell D. Miller, Andrew T. Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Silvya Oommachen, Jessica Paulsen, Christina Puckett, Ron Reyes, Christopher L. Rife, Natasha Sefcovic, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Tiffany Wooten, Qingping Xu, Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

KPN03535 is a protein unique to K. pneumoniae. The crystal structure reveals that KPN03535 represents a novel variant of the OB-fold and is likely to be a DNA-binding lipoprotein.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1254–1260. Published online 2009 October 27. doi: 10.1107/S1744309109018168
PMCID:
PMC2954213

Human Gut Microbiome

Peter J. Turnbaugh, Bernard Henrissat, Jeffrey I. Gordon

Metagenomics has unleashed a deluge of sequencing data describing the organismal, genetic, and transcriptional diversity of the human microbiome. To better understand the precise functions of the myriad proteins encoded by the microbiome, including carbohydrate-active enzymes, it will be critical to combine structural studies with functional analyses.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1261–1264. Published online 2010 July 31. doi: 10.1107/S1744309110029088
PMCID:
PMC2954214
Debanu Das, Robert D. Finn, Dennis Carlton, Mitchell D. Miller, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Constantina Bakolitsa, Connie Chen, Hsiu-Ju Chiu, Michelle Chiu, Thomas Clayton, Marc C. Deller, Lian Duan, Kyle Ellrott, Dustin Ernst, Carol L. Farr, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, Abhinav Kumar, David Marciano, Daniel McMullan, Andrew T. Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Christina Puckett, Ron Reyes, Christopher L. Rife, Natasha Sefcovic, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Tiffany Wooten, Qingping Xu, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structure of the BVU2987 gene product from B. vulgatus (UniProt A6L4L1) reveals that members of the new Pfam family PF11396 (domain of unknown function; DUF2874) are similar to β-lactamase inhibitor protein and YpmB.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1265–1273. Published online 2010 March 5. doi: 10.1107/S1744309109046788
PMCID:
PMC2954215
Constantina Bakolitsa, Qingping Xu, Christopher L. Rife, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Dennis Carlton, Connie Chen, Hsiu-Ju Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Kyle Ellrott, Carol L. Farr, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, Abhinav Kumar, Winnie W. Lam, David Marciano, Daniel McMullan, Mitchell D. Miller, Andrew T. Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Christina Puckett, Ron Reyes, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structure of BT_3984, a SusD-family protein, reveals a TPR N-terminal region providing support for a loop-rich C-terminal subdomain and suggests possible interfaces involved in sus complex formation.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1274–1280. Published online 2010 September 22. doi: 10.1107/S1744309110032999
PMCID:
PMC2954216
Qingping Xu, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Constantina Bakolitsa, Xiaohui Cai, Dennis Carlton, Connie Chen, Hsiu-Ju Chiu, Michelle Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Kyle Ellrott, Carol L. Farr, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, Abhinav Kumar, David Marciano, Daniel McMullan, Mitchell D. Miller, Andrew T. Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Christina Puckett, Ron Reyes, Natasha Sefcovic, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Tiffany Wooten, Andrew Yeh, Jiadong Zhou, Keith O. Hodgson, John Wooley, Marc-Andre Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structure of BT1062 from Bacteroides thetaiotaomicron revealed a conserved fold that is widely adopted by fimbrial components.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1281–1286. Published online 2010 July 6. doi: 10.1107/S1744309110006548
PMCID:
PMC2954217
Andrew P. Yeh, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Constantina Bakolitsa, Xiaohui Cai, Dennis Carlton, Connie Chen, Hsiu-Ju Chiu, Michelle Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Kyle Ellrott, Carol L. Farr, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, Abhinav Kumar, Winnie W. Lam, David Marciano, Daniel McMullan, Mitchell D. Miller, Andrew T. Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Christina Puckett, Ron Reyes, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Tiffany Wooten, Qingping Xu, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structure of BT2081 from B. thetaiotaomicron reveals a two-domain protein with a putative carbohydrate-binding site in the C-­terminal domain.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1287–1296. Published online 2010 August 4. doi: 10.1107/S1744309110028228
PMCID:
PMC2954218
Qingping Xu, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Constantina Bakolitsa, Xiaohui Cai, Dennis Carlton, Connie Chen, Hsiu-Ju Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Kyle Ellrott, Carol L. Farr, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, Abhinav Kumar, Winnie W. Lam, David Marciano, Mitchell D. Miller, Andrew T. Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Christina Puckett, Ron Reyes, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Tiffany Wooten, Andrew Yeh, Jiadong Zhou, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structure of a novel MACPF protein, which may play a role in the adaptation of commensal bacteria to host environments in the human gut, was determined and analyzed.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1297–1305. Published online 2010 July 31. doi: 10.1107/S1744309110023055
PMCID:
PMC2954219

Ligands That Aid in Function Characterization

Anna E. Speers, Benjamin F. Cravatt

An overview and commentary on the value of liganded structures emerging from the JCSG structural genomics initiative.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1306–1308. Published online 2010 September 30. doi: 10.1107/S1744309110035748
PMCID:
PMC2954220
Abhinav Kumar, Hsiu-Ju Chiu, Herbert L. Axelrod, Andrew Morse, Marc-André Elsliger, Ian A. Wilson, Ashley Deacon

A survey of the types and frequency of ligands that are bound to PSI structures is analyzed as well as their utility in functional annotation of previously uncharacterized proteins.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1309–1316. Published online 2010 July 6. doi: 10.1107/S1744309110008092
PMCID:
PMC2954221
Hsiu-Ju Chiu, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Dennis Carlton, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, Abhinav Kumar, David Marciano, Daniel McMullan, Mitchell D. Miller, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Ron Reyes, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Qingping Xu, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structure of the prephenate dehydrogenase component of the bifunctional H. influenzae TyrA reveals unique structural differences between bifunctional and monofunctional TyrA enzymes.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1317–1325. Published online 2010 July 31. doi: 10.1107/S1744309110021688
PMCID:
PMC2954222
Gye Won Han, Xiang-Lei Yang, Daniel McMullan, Yeeting E. Chong, S. Sri Krishna, Christopher L. Rife, Dana Weekes, Scott M. Brittain, Polat Abdubek, Eileen Ambing, Tamara Astakhova, Herbert L. Axelrod, Dennis Carlton, Jonathan Caruthers, Hsiu-Ju Chiu, Thomas Clayton, Lian Duan, Julie Feuerhelm, Joanna C. Grant, Slawomir K. Grzechnik, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Abhinav Kumar, David Marciano, Mitchell D. Miller, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Jessica Paulsen, Ron Reyes, Henry van den Bedem, Aprilfawn White, Guenter Wolf, Qingping Xu, Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Marc-André Elsliger, Paul Schimmel, Ian A. Wilson

The crystal structure of tryptophanyl-tRNA synthetase from T. maritima unexpectedly revealed an iron–sulfur cluster bound to the tRNA anticodon-binding region.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1326–1334. Published online 2010 September 23. doi: 10.1107/S1744309110037619
PMCID:
PMC2954223
Herbert L. Axelrod, Debanu Das, Polat Abdubek, Tamara Astakhova, Constantina Bakolitsa, Dennis Carlton, Connie Chen, Hsiu-Ju Chiu, Thomas Clayton, Marc C. Deller, Lian Duan, Kyle Ellrott, Carol L. Farr, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, Abhinav Kumar, Winnie W. Lam, David Marciano, Daniel McMullan, Mitchell D. Miller, Andrew T. Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Christina Puckett, Ron Reyes, Natasha Sefcovic, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Tiffany Wooten, Qingping Xu, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The first structures from the FmdE Pfam family (PF02663) reveal that some members of this family form tightly intertwined dimers consisting of two domains (N-terminal α+β core and C-terminal zinc-finger domains), whereas others contain only the core domain. The presence of the zinc-finger domain suggests that some members of this family may perform functions associated with transcriptional

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Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1335–1346. Published online 2010 August 4. doi: 10.1107/S1744309110020166
PMCID:
PMC2954224
Herbert L. Axelrod, Piotr Kozbial, Daniel McMullan, S. Sri Krishna, Mitchell D. Miller, Polat Abdubek, Claire Acosta, Tamara Astakhova, Dennis Carlton, Jonathan Caruthers, Hsiu-Ju Chiu, Thomas Clayton, Marc C. Deller, Lian Duan, Ylva Elias, Julie Feuerhelm, Slawomir K. Grzechnik, Joanna C. Grant, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Abhinav Kumar, David Marciano, Andrew T. Morse, Kevin D. Murphy, Edward Nigoghossian, Linda Okach, Silvya Oommachen, Jessica Paulsen, Ron Reyes, Christopher L. Rife, Henry J. Tien, Christina V. Trout, Henry van den Bedem, Dana Weekes, Aprilfawn White, Qingping Xu, Chloe Zubieta, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structure of an RmlC-type cupin with zinc acetate bound at the putative active site reveals significant differences from a previous structure without any bound ligand. The functional implications of the ligand-induced conformational changes are discussed.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1347–1353. Published online 2009 October 27. doi: 10.1107/S1744309109021988
PMCID:
PMC2954225
Qingping Xu, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Constantina Bakolitsa, Xiaohui Cai, Dennis Carlton, Connie Chen, Hsiu-Ju Chiu, Michelle Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Kyle Ellrott, Carol L. Farr, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, Abhinav Kumar, Winnie W. Lam, David Marciano, Mitchell D. Miller, Andrew T. Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Christina Puckett, Ron Reyes, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Tiffany Wooten, Andrew Yeh, Keith O. Hodgson, John Wooley, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

The crystal structure of the highly specific γ-d-glutamyl-l-diamino acid endopeptidase YkfC from Bacillus cereus in complex with l-Ala-γ-d-Glu reveals the structural basis for the substrate specificity of NlpC/P60-family cysteine peptidases.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1354–1364. Published online 2010 July 27. doi: 10.1107/S1744309110021214
PMCID:
PMC2954226

NMR in a high-throughput environment

Kurt Wüthrich

As an introduction to three papers on comparisons of corresponding crystal and NMR solution structures determined by the Joint Center for Structural Genomics (JCSG), an outline is provided of the JCSG strategy for combined use of the two techniques. A special commentary addresses the potentialities of the concept of ‘reference crystal structures’, which is introduced in the following

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Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1365–1366. Published online 2010 September 30. doi: 10.1107/S1744309110030320
PMCID:
PMC2954227
Kristaps Jaudzems, Michael Geralt, Pedro Serrano, Biswaranjan Mohanty, Reto Horst, Bill Pedrini, Marc-André Elsliger, Ian A. Wilson, Kurt Wüthrich

Comparison of the NMR and crystal structures of a protein determined using largely automated methods has enabled the interpretation of local differences in the highly similar structures. These differences are found in segments of higher B values in the crystal and correlate with dynamic processes on the NMR chemical shift timescale observed in solution.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1367–1380. Published online 2010 July 6. doi: 10.1107/S1744309110005890
PMCID:
PMC2954228
Biswaranjan Mohanty, Pedro Serrano, Bill Pedrini, Kristaps Jaudzems, Michael Geralt, Reto Horst, Torsten Herrmann, Marc-André Elsliger, Ian A. Wilson, Kurt Wüthrich

NMR structures of the proteins TM1112 and TM1367 solved by the JCSG in solution at 298 K could be superimposed with the corresponding crystal structures at 100 K with r.m.s.d. values of <1.0 Å for the backbone heavy atoms. For both proteins the structural differences between multiple molecules in the asymmetric unit of the crystals correlated with structural

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Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1381–1392. Published online 2010 August 7. doi: 10.1107/S1744309110020956
PMCID:
PMC2954229
Pedro Serrano, Bill Pedrini, Michael Geralt, Kristaps Jaudzems, Biswaranjan Mohanty, Reto Horst, Torsten Herrmann, Marc-André Elsliger, Ian A. Wilson, Kurt Wüthrich

Tools for systematic comparisons of NMR and crystal structures developed by the JCSG were applied to two proteins with known functions: the T. maritima anti-σ factor antagonist TM1081 and the mouse γ-glutamylamine cyclotransferase A2LD1 (gi:13879369). In an attempt to exploit the complementarity of crystal and NMR data, the combined use of the two structure-determination techniques

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Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1393–1405. Published online 2010 September 30. doi: 10.1107/S1744309110033658
PMCID:
PMC2954230

Articles from Acta Crystallographica Section F: Structural Biology and Crystallization Communications are provided here courtesy of International Union of Crystallography