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The Open Protein Structure Annotation Network
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3dee

    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
    Ligands
    Metals

    Jmol

     
    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
     
    18. OTHER STRUCTURE-BASED DATABASES
    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

    Reviews

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