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(-) Description

Title :  CRYSTAL STRUCTURE OF COLLAGENASE G FROM CLOSTRIDIUM HISTOLYTICUM IN COMPLEX WITH ISOAMYLPHOSPHONYL-GLY-PRO-ALA AT 3.25 ANGSTROM RESOLUTION
 
Authors :  U. Eckhard, H. Brandstetter
Date :  21 Jan 11  (Deposition) - 28 Sep 11  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase-Inhibitor Complex, Hydrolase, Gluzincin, Metalloprotease (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

(-) Compounds

Molecule 1 - COLLAGENASE
    Chains: A
    EC Number: 3.4.24.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-15B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 119-880
    Organism Scientific: CLOSTRIDIUM HISTOLYTICUM
    Organism Taxid: 1498
    Synonym: COLLAGENASE G
 
Molecule 2 - ISOAMYLPHOSPHONYL-GLY-PRO-ALA
    Chains: B
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric/Biological Unit (6, 9)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2FLC1Ligand/IonCITRATE ANION
3IPI1Mod. Amino Acid3-METHYLBUTYLPHOSPHONIC ACID
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
6ZN1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:523 , HIS A:527 , GLU A:555 , HOH A:2042 , IPI B:1BINDING SITE FOR RESIDUE ZN A1791
2AC2SOFTWARESER A:568 , TYR A:618 , MET A:622 , TRP A:736 , ASP A:737 , SER A:740 , LYS A:741BINDING SITE FOR RESIDUE FLC A1793
3AC3SOFTWARELYS A:247 , ASN A:251 , LYS A:291 , PHE A:295BINDING SITE FOR RESIDUE TRS A1794
4AC4SOFTWARETHR A:565 , ARG A:566 , THR A:567 , SER A:568 , LEU A:675BINDING SITE FOR RESIDUE TRS A1795
5AC5SOFTWAREASP A:368 , HOH A:2043BINDING SITE FOR RESIDUE TRS A1796
6AC6SOFTWAREALA A:458 , LEU A:459 , ASN A:634BINDING SITE FOR RESIDUE PEG A1797
7AC7SOFTWAREGLU A:619BINDING SITE FOR RESIDUE PEG A1798
8AC8SOFTWAREALA A:277 , PRO A:278 , ASP A:279 , THR A:284 , TRP A:337 , ASP A:340 , HOH A:2044BINDING SITE FOR RESIDUE 1PE A1799

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y6I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y6I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y6I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y6I)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y6I)

(-) Sequences/Alignments

Asymmetric/Biological 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:671
 aligned with Q9X721_HATHI | Q9X721 from UniProtKB/TrEMBL  Length:1118

    Alignment length:674
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786    
         Q9X721_HATHI   117 EKYDFEYLNGLSYTELTNLIKNIKWNQINGLFNYSTGSQKFFGDKNRVQAIINALQESGRTYTANDMKGIETFTEVLRAGFYLGYYNDGLSYLNDRNFQDKCIPAMIAIQKNPNFKLGTAVQDEVITSLGKLIGNASANAEVVNNCVPVLKQFRENLNQYAPDYVKGTAVNELIKGIEFDFSGAAYEKDVKTMPWYGKIDPFINELKALGLYGNITSATEWASDVGIYYLSKFGLYSTNRNDIVQSLEKAVDMYKYGKIAFVAMERITWDYDGIGSNGKKVDHDKFLDDAEKHYLPKTYTFDNGTFIIRAGDKVSEEKIKRLYWASREVKSQFHRVVGNDKALEVGNADDVLTMKIFNSPEEYKFNTNINGVSTDNGGLYIEPRGTFYTYERTPQQSIFSLEELFRHEYTHYLQARYLVDGLWGQGPFYEKNRLTWFDEGTAEFFAGSTRTSGVLPRKSILGYLAKDKVDHRYSLKKTLNSGYDDSDWMFYNYGFAVAHYLYEKDMPTFIKMNKAILNTDVKSYDEIIKKLSDDANKNTEYQNHIQELADKYQGAGIPLVSDDYLKDHGYKKASEVYSEISKAASLTNTSVTAEKSQYFNTFTLRGTYTGETSKGEFKDWDEMSKKLDGTLESLAKNSWSGYKTLTAYFTNYRVTSDNKVQYDVVFHGVLTDNA 790
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhhhhhhh........hhhhheeeeee.hhhhhhhhhhhhh.......eeehhh.eeeee.........hhhhhhhhhhhhhhhhhhh.......hhhhhh..hhhhhhhhhhhhh..........hhhhhhhhh........hhhhhhh.---....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.....hhhhhhhhhhhhh.eeeeeeeeee....eeeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh...hhhhhhheeeeeeeee....eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6i A 117 TMYDFEYLNGLSYTELTNLIKNIKWNQINGLFNYSTGSQKFFGDKNRVQAIINALQESGRTYTANDMKGIETFTEVLRAGFYLGYYNDGLSYLNDRNFQDKCIPAMIAIQKNPNFKLGTAVQDEVITSLGKLIGNASANAEVVNNCVPVLKQFRENLNQYAPDYVKGTAVNELIKGIEFDFSGAAYEKDVKTMPWYGKIDPFINELKALGLYGNITSATEWASDVGIYYLSKFGLYSTNRNDIVQSLEKAVDMYKYGKIAFVAMERITWDYDGIGSNGKKVDHDKFLDDAEKHYLPKTYTFDNGTFIIRAGDKVSEEKIKRLYWASREVKSQFHRVVGNDKALEVGNADDVLTMKIFNSPEEYKFNTNINGVSTDNGGLYIEPRGTFYTYERTPQQSIFSLEELFRHEYTHYLQARYLVDGLWGQGPFYEKNRLTWFDEGTAEFFAGSTRTSGVLPRKLILGYLAKDKVDHRYSLKKTLNS---DSDWMFYNYGFAVAHYLYEKDMPTFIKMNKAILNTDVKSYDEIIKKLSDDANKNTEYQNHIQELVDKYQGAGIPLVSDDYLKDHGYKKASEVYSEISKAASLTNTSVTAEKSQYFNTFTLRGTYTGETSKGEFKDWDEMSKKLDGTLESLAKNSWSGYKTLTAYFTNYRVTSDNKVQYDVVFHGVLTDNG 790
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596|   |  606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          597 601                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2y6i B   1 xGPA   4
                            |   
                            1-IPI
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 2Y6I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y6I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y6I)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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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  3.4.24.3
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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 2y72 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