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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PKD DOMAIN OF COLLAGENASE G FROM CLOSTRIDIUM HISTOLYTICUM AT 1.18 ANGSTROM RESOLUTION.
 
Authors :  U. Eckhard, H. Brandstetter
Date :  27 Jan 11  (Deposition) - 28 Sep 11  (Release) - 19 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.18
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Polycystic Kidney Disease Domain, Beta Barrel, Collagen Recognition Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Eckhard, E. Schoenauer, D. Nuess, H. Brandstetter
Structure Of Collagenase G Reveals A Chew-And -Digest Mechanism Of Bacterial Collagenolysis
Nat. Struct. Mol. Biol. V. 18 1109 2011
PubMed-ID: 21947205  |  Reference-DOI: 10.1038/NSMB.2127
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLLAGENASE
    Chains: A, B
    EC Number: 3.4.24.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Fragment: POLYCYSTIC KIDNEY DISEASE (PKD) DOMAIN, RESIDUES 799-880
    Organism Scientific: CLOSTRIDIUM HISTOLYTICUM
    Organism Taxid: 1498
    Synonym: COLLAGENASE G

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2Y72)

(-) Sites  (0, 0)

(no "Site" information available for 2Y72)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y72)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y72)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y72)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y72)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y72)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:85
 aligned with Q9X721_HATHI | Q9X721 from UniProtKB/TrEMBL  Length:1118

    Alignment length:85
                                   805       815       825       835       845       855       865       875     
         Q9X721_HATHI   796 KAPIAKVTGPSTGAVGRNIEFSGKDSKDEDGKIVSYDWDFGDGATSRGKNSVHAYKKAGTYNVTLKVTDDKGATATESFTIEIKN 880
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.eee...eeeee..........eeeeeee.....eee..eeeee....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 2y72 A 796 GGTIAKVTGPSTGAVGRNIEFSGKDSKDEDGKIVSYDWDFGDGATSRGKNSVHAYKKAGTYNVTLKVTDDKGATATESFTIEIKN 880
                                   805       815       825       835       845       855       865       875     


Chain B from PDB  Type:PROTEIN  Length:85
 aligned with Q9X721_HATHI | Q9X721 from UniProtKB/TrEMBL  Length:1118

    Alignment length:85
                                   805       815       825       835       845       855       865       875     
         Q9X721_HATHI   796 KAPIAKVTGPSTGAVGRNIEFSGKDSKDEDGKIVSYDWDFGDGATSRGKNSVHAYKKAGTYNVTLKVTDDKGATATESFTIEIKN 880
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.eee...eeeee..........eeeeeee.....eee..eeeee....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 2y72 B 796 GGTIAKVTGPSTGAVGRNIEFSGKDSKDEDGKIVSYDWDFGDGATSRGKNSVHAYKKAGTYNVTLKVTDDKGATATESFTIEIKN 880
                                   805       815       825       835       845       855       865       875
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2Y72)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y72)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y72)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9X721_HATHI | Q9X721)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        Q9X721_HATHI | Q9X721: 2o8o
UniProtKB/TrEMBL
        Q9X721_HATHI | Q9X721: 2y3u 2y50 2y6i 4aqo 4are 4hpk 4jrw 4tn9 5iku

(-) Related Entries Specified in the PDB File

2y3u CRYSTAL STRUCTURE OF APO COLLAGENASE G FROM CLOSTRIDIUM HISTOLYTICUM AT 2.55 ANGSTROM RESOLUTION
2y50 CRYSTAL STRUCTURE OF COLLAGENASE G FROM CLOSTRIDIUM HISTOLYTICUM AT 2.80 ANGSTROM RESOLUTION
2y6i CRYSTAL STRUCTURE OF COLLAGENASE G FROM CLOSTRIDIUM HISTOLYTICUM IN COMPLEX WITH ISOAMYLPHOSPHONYL-GLY-PRO-ALA AT 3.25 ANGSTROM RESOLUTION