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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COLLAGENASE UNIT OF COLLAGENASE G FROM CLOSTRIDIUM HISTOLYTICUM AT 2.19 ANGSTROM RESOLUTION.
 
Authors :  U. Eckhard, H. Brandstetter
Date :  23 Apr 12  (Deposition) - 05 Jun 13  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Collagen, Peptidase, Collagenolysis, Metalloprotease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Eckhard, E. Schonauer, H. Brandstetter
Structural Basis For Activity Regulation And Substrate Preference Of Clostridial Collagenases G, H, And T.
J. Biol. Chem. V. 288 20184 2013
PubMed-ID: 23703618  |  Reference-DOI: 10.1074/JBC.M112.448548
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLLAGENASE G
    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: COLLAGENASE UNIT, RESIDUES 119-790
    Organism Scientific: CLOSTRIDIUM HISTOLYTICUM
    Organism Taxid: 1498

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2P6G1Ligand/IonHEXAETHYLENE GLYCOL
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:523 , GLU A:524 , HIS A:527 , GLU A:555 , HOH A:2168 , HOH A:2169BINDING SITE FOR RESIDUE ZN A1790
2AC2SOFTWAREPRO A:278 , ASP A:279 , TYR A:280 , TRP A:337 , ASP A:340 , TYR A:344 , HOH A:2267BINDING SITE FOR RESIDUE P6G A1791
3AC3SOFTWARESER A:568 , VAL A:570 , TYR A:618 , GLU A:619 , MET A:622 , TRP A:736 , ASP A:737 , LYS A:741 , HOH A:2117 , HOH A:2196 , HOH A:2251BINDING SITE FOR RESIDUE FLC A1792
4AC4SOFTWARETYR A:344 , LYS A:348 , ARG A:382 , TRP A:385 , HOH A:2269BINDING SITE FOR RESIDUE TRS A1793

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ARE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ARE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ARE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ARE)

(-) Exons   (0, 0)

(no "Exon" information available for 4ARE)

(-) 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:678
 aligned with Q9X721_HATHI | Q9X721 from UniProtKB/TrEMBL  Length:1118

    Alignment length:680
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789
         Q9X721_HATHI   110 SIANTNSEKYDFEYLNGLSYTELTNLIKNIKWNQINGLFNYSTGSQKFFGDKNRVQAIINALQESGRTYTANDMKGIETFTEVLRAGFYLGYYNDGLSYLNDRNFQDKCIPAMIAIQKNPNFKLGTAVQDEVITSLGKLIGNASANAEVVNNCVPVLKQFRENLNQYAPDYVKGTAVNELIKGIEFDFSGAAYEKDVKTMPWYGKIDPFINELKALGLYGNITSATEWASDVGIYYLSKFGLYSTNRNDIVQSLEKAVDMYKYGKIAFVAMERITWDYDGIGSNGKKVDHDKFLDDAEKHYLPKTYTFDNGTFIIRAGDKVSEEKIKRLYWASREVKSQFHRVVGNDKALEVGNADDVLTMKIFNSPEEYKFNTNINGVSTDNGGLYIEPRGTFYTYERTPQQSIFSLEELFRHEYTHYLQARYLVDGLWGQGPFYEKNRLTWFDEGTAEFFAGSTRTSGVLPRKSILGYLAKDKVDHRYSLKKTLNSGYDDSDWMFYNYGFAVAHYLYEKDMPTFIKMNKAILNTDVKSYDEIIKKLSDDANKNTEYQNHIQELADKYQGAGIPLVSDDYLKDHGYKKASEVYSEISKAASLTNTSVTAEKSQYFNTFTLRGTYTGETSKGEFKDWDEMSKKLDGTLESLAKNSWSGYKTLTAYFTNYRVTSDNKVQYDVVFHGVLTDN 789
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....--...hhhhhh..hhhhhhhhhhh.hhhh.......hhhhhhhh.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhhhhhhh........hhhhheeeeee.hhhhhhhhhhhhh......eeeehhh.eeeee.........hhhhhhhhhhhhhhhhhhh.......hhhhh...hhhhhhhhhhhhh..........hhhhhhhhh........hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.....hhhhhhhhhhhhh..eeeeeeeee....eeeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh...hhhhhhheeeeeeeee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4are A 110 NLYFQ--TMYDFEYLNGLSYTELTNLIKNIKWNQINGLFNYSTGSQKFFGDKNRVQAIINALQESGRTYTANDMKGIETFTEVLRAGFYLGYYNDGLSYLNDRNFQDKCIPAMIAIQKNPNFKLGTAVQDEVITSLGKLIGNASANAEVVNNCVPVLKQFRENLNQYAPDYVKGTAVNELIKGIEFDFSGAAYEKDVKTMPWYGKIDPFINELKALGLYGNITSATEWASDVGIYYLSKFGLYSTNRNDIVQSLEKAVDMYKYGKIAFVAMERITWDYDGIGSNGKKVDHDKFLDDAEKHYLPKTYTFDNGTFIIRAGDKVSEEKIKRLYWASREVKSQFHRVVGNDKALEVGNADDVLTMKIFNSPEEYKFNTNINGVSTDNGGLYIEPRGTFYTYERTPQQSIFSLEELFRHEYTHYLQARYLVDGLWGQGPFYEKNRLTWFDEGTAEFFAGSTRTSGVLPRKLILGYLAKDKVDHRYSLKKTLNSGYDDSDWMFYNYGFAVAHYLYEKDMPTFIKMNKAILNTDVKSYDEIIKKLSDDANKNTEYQNHIQELVDKYQGAGIPLVSDDYLKDHGYKKASEVYSEISKAASLTNTSVTAEKSQYFNTFTLRGTYTGETSKGEFKDWDEMSKKLDGTLESLAKNSWSGYKTLTAYFTNYRVTSDNKVQYDVVFHGVLTDN 789
                                |  119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789
                              114  |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
                                 117
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4ARE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ARE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ARE)

(-) 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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  4are
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  Q9X721_HATHI | Q9X721
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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 2y6i 2y72 4aqo 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
2y72 CRYSTAL STRUCTURE OF THE PKD DOMAIN OF COLLAGENASE G FROM CLOSTRIDIUM HISTOLYTICUM AT 1.18 ANGSTROM RESOLUTION.
4aqo CRYSTAL STRUCTURE OF THE CALCIUM BOUND PKD-LIKE DOMAIN OF COLLAGENASE G FROM CLOSTRIDIUM HISTOLYTICUM AT 0. 99 ANGSTROM RESOLUTION.
4ar9 CRYSTAL STRUCTURE OF THE PEPTIDASE DOMAIN OF COLLAGENASE T FROM CLOSTRIDIUM TETANI AT 1.69 ANGSTROM RESOLUTION.
4arf CRYSTAL STRUCTURE OF THE PEPTIDASE DOMAIN OF COLLAGENASE H FROM CLOSTRIDIUM HISTOLYTICUM IN COMPLEX WITH THE PEPTIDIC INHIBITOR ISOAMYLPHOSPHONYL-GLY-PRO-ALA AT 1. 77 ANGSTROM RESOLUTION.