The Open Protein Structure Annotation Network
PDB Keyword


    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation. Acta Crystallogr.,Sect.F 66 1174-1181 2010
    Site JCSG
    PDB Id 3dee Target Id 389948
    Molecular Characteristics
    Source Neisseria gonorrhoeae fa 1090
    Alias Ids TPS7638,YP_208969.1, BIG_448, 88380 Molecular Weight 28577.54 Da.
    Residues 248 Isoelectric Point 4.65
    Sequence mqpetsaqyqhrfsqairggeaadglpqdrlnvyirlirnnihsfidrcytetrqyfdskewsrlkegf vrdaraqtpyfqeipgeflqycqspplsdgilalmdfeytqllaevaqipdipdihysndskytpspaa firqyrydvthdlqeaetalliwrnaeddvmyqtldgfdmmlleimgssalsfdtlaqtlvefmpkadn wknillgkwsgwieqriiipslsaisenmegnspsqnhlsa
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.10 Rfree 0.267
    Matthews' coefficent 2.28 Rfactor 0.223
    Waters 95 Solvent Content 45.96

    Ligand Information


    Google Scholar output for 3dee
    1. PDBe: protein data bank in Europe
    S Velankar, C Best, B Beuth, CH Boutselakis - Nucleic acids , 2010 - Oxford Univ Press
    2. Assessment of CASP8 structure predictions for template free targets
    M Ben_David, O Noivirt_Brik, A Paz - Proteins: Structure, , 2009 - Wiley Online Library
    3. Target domain definition and classification in CASP8
    ML Tress, I Ezkurdia - : Structure, Function, and , 2009 - Wiley Online Library
    4. Analysis of CASP8 targets, predictions and assessment methods
    SY Shi, J Pei, RI Sadreyev, LN Kinch - Database: the journal , 2009 - ncbi.nlm.nih.gov
    5. The CATH Hierarchy Revisited--Structural Divergence in Domain Superfamilies and the Continuity of Fold Space
    A Cuff, OC Redfern, L Greene, I Sillitoe, T Lewis - Structure, 2009 - Elsevier
    6. Analysis of protein contacts into Protein Units
    G Faure, A Bornot, AG De Brevern - Biochimie, 2009 - Elsevier
    7. Protein contacts, inter-residue interactions and side-chain modelling
    G Faure, A Bornot, AG de Brevern - Biochimie, 2008 - Elsevier
    8. Universality in protein residue networks
    E Estrada - Biophysical journal, 2010 - Elsevier
    9. Protein domain prediction
    H Ingolfsson, G Yona - METHODS IN MOLECULAR BIOLOGY-CLIFTON , 2008 - Springer
    10. Identifying structural domains in proteins
    S Veretnik, J Gu, S Wodak - In Genny Gu and Philip Bourne Structural , 2009 - sdsc.edu
    11. The Classification of Protein Domains
    RL Marsden, CA Orengo - METHODS IN MOLECULAR BIOLOGY- , 2008 - Springer
    12. Comparative analysis of threshold and tessellation methods for determining protein contacts
    J Esque, C Oguey, AG de Brevern - Journal of chemical , 2011 - ACS Publications
    13. The Fragment-based Consistency Score in Model Quality Assessment for De Novo Prediction of Protein Structures
    H Cetin, TN Sasaki, M Sasai - Chem-Bio Informatics Journal, 2011 - J-STAGE
    14. ___________________________________
    H Cetin_ _____ ____ - CBI _____, 2011 - J-STAGE
    15. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation
    D Das, NV Grishin, A Kumar, D Carlton - Section F: Structural , 2009 - scripts.iucr.org
    16. A bioinformatic web server to cut protein structures in terms of Protein Units.
    JC Gelly, AG de Brevern - 2011 - dsimb.inserm.fr
    17. Advanced graph mining methods for protein analysis
    YPP Chen, J Rong, G Li - Biological Data Mining, 2010 - books.google.com
    JL Fink, H Weissig, PE Bourne - Structural bioinformatics, 2009 - books.google.com
    19. Protein Multiple Sequence Alignment: Benchmarks and Comparison
    R Gharegozlou - 2009 - cmgm3.stanford.edu
    20. Automated Protein Structure Classification: A Survey
    O Hassanzadeh - Arxiv preprint arXiv:0907.1990, 2009 - arxiv.org
    21. Universit Paris VIIDenis Diderot Ecole Doctorale Inter///BIO
    V MEYER - 2009 - hal.inria.fr

    Protein Summary

    A manuscript describing this structure has been published in 2010:

    "The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation", Das, D. et. al. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1174-81.


    Gene NGO1945 from Neisseria gonorrhoeae fa 1090 encodes the YP_208969 protein that belongs to the DUF2063 (PF09836). According to the Conserved Domain Database, this protein (NGO1945) belongs to the COG3219 superfamily which includes a family of uncharacterized proteins of unknown function in bacteria. PSI-BLAST provides hits to many hypothetical proteins. There is also a sequence hit to a predicted repair protein from H. influenza (ZP_01797326, COG3219) with 34% sequence identity (e-value=2e-29) and a RNA polymerase sigma factor from H. parasuis 29755 (ZP_02478439) with 38% sequence identity (e-value=3e-34).  The genomic neighborhood analysis detects, with a 0.83 score, the presence of a RNA-polymerase sigma-70 factor (NGO1944).

    The FFAS, DALI or SSM servers do not retrieve any signficant hits with any other proteins.

    3dee protein structure can be described in 3 parts. The N-terminal part from residues 31-117 is a helical bundle with 4 main helices. This domain then merges into a middle portion consisting of a loop and a beta sheet up to ~aa 174. Finally, there is a C-terminal helical bundle of 3 helices. The overall structure reveals the protein to be roughly elongated in shape. The N-terminal 30 amino acids is missing from the final structure due to lack of electron density even though the LC-MS spectrum of the purified protein confirms that the protein was intact. There is some density in the vicinity of residue MSE169 which appears to be a peptide fragment and could be a portion of the missing N-terminus but this density has been left unmodeled due to low reliability.


    Ligand Summary




    No references found.

    Tag page

    Files (0)

    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch