The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation

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 FeuerhelmAnna 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

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from Neisseria gonorrhoeae, has been determined and reveals that the N-terminal DUF2063 domain is likely to be a DNA-binding domain. In conjunction with the rest of the protein, NGO1945 is likely to be involved in transcriptional regulation, which is consistent with genomic neighborhood analysis. Of the 216 currently known proteins that contain a DUF2063 domain, the most significant sequence homologs of NGO1945 (̃40-99% sequence identity) are from various Neisseria and Haemophilus species. As these are important human pathogens, NGO1945 represents an interesting candidate for further exploration via biochemical studies and possible therapeutic intervention.

Original languageEnglish (US)
Pages (from-to)1174-1181
Number of pages8
JournalActa Crystallographica Section F: Structural Biology and Crystallization Communications
Volume66
Issue number10
DOIs
StatePublished - Oct 2010
Externally publishedYes

Fingerprint

proteins
Haemophilus
Neisseria
Proteins
Neisseria gonorrhoeae
Pathogens
Sequence Homology
pathogens
Crystal structure
deoxyribonucleic acid
DNA
crystal structure
Therapeutics

Keywords

  • DUF2063
  • NGO1945
  • PF09836
  • putative DNA-binding proteins
  • putative transcription regulators
  • structural genomics

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Structural Biology
  • Genetics
  • Condensed Matter Physics

Cite this

The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation. / Das, Debanu; Grishin, Nick V.; Kumar, Abhinav; Carlton, Dennis; Bakolitsa, Constantina; Miller, Mitchell D.; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Burra, Prasad; Chen, Connie; Chiu, Hsiu Ju; Chiu, Michelle; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ellrott, Kyle; Ernst, Dustin; Farr, Carol L.; Feuerhelm, Julie; Grzechnik, Anna; Grzechnik, Slawomir K.; Grant, Joanna C.; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Johnson, Hope A.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Puckett, Christina; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; Van Den Bedem, Henry; Weekes, Dana; Wooten, Tiffany; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

In: Acta Crystallographica Section F: Structural Biology and Crystallization Communications, Vol. 66, No. 10, 10.2010, p. 1174-1181.

Research output: Contribution to journalArticle

Das, D, Grishin, NV, Kumar, A, Carlton, D, Bakolitsa, C, Miller, MD, Abdubek, P, Astakhova, T, Axelrod, HL, Burra, P, Chen, C, Chiu, HJ, Chiu, M, Clayton, T, Deller, MC, Duan, L, Ellrott, K, Ernst, D, Farr, CL, Feuerhelm, J, Grzechnik, A, Grzechnik, SK, Grant, JC, Han, GW, Jaroszewski, L, Jin, KK, Johnson, HA, Klock, HE, Knuth, MW, Kozbial, P, Krishna, SS, Marciano, D, McMullan, D, Morse, AT, Nigoghossian, E, Nopakun, A, Okach, L, Oommachen, S, Paulsen, J, Puckett, C, Reyes, R, Rife, CL, Sefcovic, N, Tien, HJ, Trame, CB, Van Den Bedem, H, Weekes, D, Wooten, T, Xu, Q, Hodgson, KO, Wooley, J, Elsliger, MA, Deacon, AM, Godzik, A, Lesley, SA & Wilson, IA 2010, 'The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation', Acta Crystallographica Section F: Structural Biology and Crystallization Communications, vol. 66, no. 10, pp. 1174-1181. https://doi.org/10.1107/S1744309109022672
Das, Debanu ; Grishin, Nick V. ; Kumar, Abhinav ; Carlton, Dennis ; Bakolitsa, Constantina ; Miller, Mitchell D. ; Abdubek, Polat ; Astakhova, Tamara ; Axelrod, Herbert L. ; Burra, Prasad ; Chen, Connie ; Chiu, Hsiu Ju ; Chiu, Michelle ; Clayton, Thomas ; Deller, Marc C. ; Duan, Lian ; Ellrott, Kyle ; Ernst, Dustin ; Farr, Carol L. ; Feuerhelm, Julie ; Grzechnik, Anna ; Grzechnik, Slawomir K. ; Grant, Joanna C. ; Han, Gye Won ; Jaroszewski, Lukasz ; Jin, Kevin K. ; Johnson, Hope A. ; Klock, Heath E. ; Knuth, Mark W. ; Kozbial, Piotr ; Krishna, S. Sri ; Marciano, David ; McMullan, Daniel ; Morse, Andrew T. ; Nigoghossian, Edward ; Nopakun, Amanda ; Okach, Linda ; Oommachen, Silvya ; Paulsen, Jessica ; Puckett, Christina ; Reyes, Ron ; Rife, Christopher L. ; Sefcovic, Natasha ; Tien, Henry J. ; Trame, Christine B. ; Van Den Bedem, Henry ; Weekes, Dana ; Wooten, Tiffany ; Xu, Qingping ; Hodgson, Keith O. ; Wooley, John ; Elsliger, Marc André ; Deacon, Ashley M. ; Godzik, Adam ; Lesley, Scott A. ; Wilson, Ian A. / The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation. In: Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 2010 ; Vol. 66, No. 10. pp. 1174-1181.
@article{092c0ca429354759b2b2004c910c7e40,
title = "The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation",
abstract = "Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from Neisseria gonorrhoeae, has been determined and reveals that the N-terminal DUF2063 domain is likely to be a DNA-binding domain. In conjunction with the rest of the protein, NGO1945 is likely to be involved in transcriptional regulation, which is consistent with genomic neighborhood analysis. Of the 216 currently known proteins that contain a DUF2063 domain, the most significant sequence homologs of NGO1945 (̃40-99{\%} sequence identity) are from various Neisseria and Haemophilus species. As these are important human pathogens, NGO1945 represents an interesting candidate for further exploration via biochemical studies and possible therapeutic intervention.",
keywords = "DUF2063, NGO1945, PF09836, putative DNA-binding proteins, putative transcription regulators, structural genomics",
author = "Debanu Das and Grishin, {Nick V.} and Abhinav Kumar and Dennis Carlton and Constantina Bakolitsa and Miller, {Mitchell D.} and Polat Abdubek and Tamara Astakhova and Axelrod, {Herbert L.} and Prasad Burra and Connie Chen and Chiu, {Hsiu Ju} and Michelle Chiu and Thomas Clayton and Deller, {Marc C.} and Lian Duan and Kyle Ellrott and Dustin Ernst and Farr, {Carol L.} and Julie Feuerhelm and Anna Grzechnik and Grzechnik, {Slawomir K.} and Grant, {Joanna C.} and Han, {Gye Won} and Lukasz Jaroszewski and Jin, {Kevin K.} and Johnson, {Hope A.} and Klock, {Heath E.} and Knuth, {Mark W.} and Piotr Kozbial and Krishna, {S. Sri} and David Marciano and Daniel McMullan and Morse, {Andrew T.} and Edward Nigoghossian and Amanda Nopakun and Linda Okach and Silvya Oommachen and Jessica Paulsen and Christina Puckett and Ron Reyes and Rife, {Christopher L.} and Natasha Sefcovic and Tien, {Henry J.} and Trame, {Christine B.} and {Van Den Bedem}, Henry and Dana Weekes and Tiffany Wooten and Qingping Xu and Hodgson, {Keith O.} and John Wooley and Elsliger, {Marc Andr{\'e}} and Deacon, {Ashley M.} and Adam Godzik and Lesley, {Scott A.} and Wilson, {Ian A.}",
year = "2010",
month = "10",
doi = "10.1107/S1744309109022672",
language = "English (US)",
volume = "66",
pages = "1174--1181",
journal = "Acta Crystallographica Section F:Structural Biology Communications",
issn = "1744-3091",
publisher = "John Wiley and Sons Ltd",
number = "10",

}

TY - JOUR

T1 - The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation

AU - Das, Debanu

AU - Grishin, Nick V.

AU - Kumar, Abhinav

AU - Carlton, Dennis

AU - Bakolitsa, Constantina

AU - Miller, Mitchell D.

AU - Abdubek, Polat

AU - Astakhova, Tamara

AU - Axelrod, Herbert L.

AU - Burra, Prasad

AU - Chen, Connie

AU - Chiu, Hsiu Ju

AU - Chiu, Michelle

AU - Clayton, Thomas

AU - Deller, Marc C.

AU - Duan, Lian

AU - Ellrott, Kyle

AU - Ernst, Dustin

AU - Farr, Carol L.

AU - Feuerhelm, Julie

AU - Grzechnik, Anna

AU - Grzechnik, Slawomir K.

AU - Grant, Joanna C.

AU - Han, Gye Won

AU - Jaroszewski, Lukasz

AU - Jin, Kevin K.

AU - Johnson, Hope A.

AU - Klock, Heath E.

AU - Knuth, Mark W.

AU - Kozbial, Piotr

AU - Krishna, S. Sri

AU - Marciano, David

AU - McMullan, Daniel

AU - Morse, Andrew T.

AU - Nigoghossian, Edward

AU - Nopakun, Amanda

AU - Okach, Linda

AU - Oommachen, Silvya

AU - Paulsen, Jessica

AU - Puckett, Christina

AU - Reyes, Ron

AU - Rife, Christopher L.

AU - Sefcovic, Natasha

AU - Tien, Henry J.

AU - Trame, Christine B.

AU - Van Den Bedem, Henry

AU - Weekes, Dana

AU - Wooten, Tiffany

AU - Xu, Qingping

AU - Hodgson, Keith O.

AU - Wooley, John

AU - Elsliger, Marc André

AU - Deacon, Ashley M.

AU - Godzik, Adam

AU - Lesley, Scott A.

AU - Wilson, Ian A.

PY - 2010/10

Y1 - 2010/10

N2 - Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from Neisseria gonorrhoeae, has been determined and reveals that the N-terminal DUF2063 domain is likely to be a DNA-binding domain. In conjunction with the rest of the protein, NGO1945 is likely to be involved in transcriptional regulation, which is consistent with genomic neighborhood analysis. Of the 216 currently known proteins that contain a DUF2063 domain, the most significant sequence homologs of NGO1945 (̃40-99% sequence identity) are from various Neisseria and Haemophilus species. As these are important human pathogens, NGO1945 represents an interesting candidate for further exploration via biochemical studies and possible therapeutic intervention.

AB - Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from Neisseria gonorrhoeae, has been determined and reveals that the N-terminal DUF2063 domain is likely to be a DNA-binding domain. In conjunction with the rest of the protein, NGO1945 is likely to be involved in transcriptional regulation, which is consistent with genomic neighborhood analysis. Of the 216 currently known proteins that contain a DUF2063 domain, the most significant sequence homologs of NGO1945 (̃40-99% sequence identity) are from various Neisseria and Haemophilus species. As these are important human pathogens, NGO1945 represents an interesting candidate for further exploration via biochemical studies and possible therapeutic intervention.

KW - DUF2063

KW - NGO1945

KW - PF09836

KW - putative DNA-binding proteins

KW - putative transcription regulators

KW - structural genomics

UR - http://www.scopus.com/inward/record.url?scp=77958056031&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77958056031&partnerID=8YFLogxK

U2 - 10.1107/S1744309109022672

DO - 10.1107/S1744309109022672

M3 - Article

C2 - 20944208

AN - SCOPUS:77958056031

VL - 66

SP - 1174

EP - 1181

JO - Acta Crystallographica Section F:Structural Biology Communications

JF - Acta Crystallographica Section F:Structural Biology Communications

SN - 1744-3091

IS - 10

ER -