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(-) Description

Title :  CRYSTAL STRUCTURE OF APO COLLAGENASE G FROM CLOSTRIDIUM HISTOLYTICUM AT 2.55 ANGSTROM RESOLUTION
 
Authors :  U. Eckhard, H. Brandstetter
Date :  26 Dec 10  (Deposition) - 28 Sep 11  (Release) - 19 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A
Keywords :  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: B834
    Expression System Taxid: 562
    Expression System Vector: PET-15B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 119-880
    Organism Scientific: CLOSTRIDIUM HISTOLYTICUM
    Organism Taxid: 1498
    Synonym: COLLAGENASE G

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2MSE11Mod. Amino AcidSELENOMETHIONINE
3P6G1Ligand/IonHEXAETHYLENE GLYCOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:277 , PRO A:278 , TYR A:280 , ASN A:287 , VAL A:341 , HOH A:2080 , HOH A:2081BINDING SITE FOR RESIDUE P6G A1792
2AC2SOFTWARESER A:568 , TYR A:618 , MSE A:622 , TRP A:736 , ASP A:737 , SER A:740 , HOH A:2082BINDING SITE FOR RESIDUE FLC A1793
3AC3SOFTWAREHOH A:2083BINDING SITE FOR RESIDUE PEG A1794

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y3U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y3U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y3U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y3U)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y3U)

(-) 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:679
 aligned with Q9X721_HATHI | Q9X721 from UniProtKB/TrEMBL  Length:1118

    Alignment length:681
                                   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 SIANTNSEKYDFEYLNGLSYTELTNLIKNIKWNQINGLFNYSTGSQKFFGDKNRVQAIINALQESGRTYTANDMKGIETFTEVLRAGFYLGYYNDGLSYLNDRNFQDKCIPAMIAIQKNPNFKLGTAVQDEVITSLGKLIGNASANAEVVNNCVPVLKQFRENLNQYAPDYVKGTAVNELIKGIEFDFSGAAYEKDVKTMPWYGKIDPFINELKALGLYGNITSATEWASDVGIYYLSKFGLYSTNRNDIVQSLEKAVDMYKYGKIAFVAMERITWDYDGIGSNGKKVDHDKFLDDAEKHYLPKTYTFDNGTFIIRAGDKVSEEKIKRLYWASREVKSQFHRVVGNDKALEVGNADDVLTMKIFNSPEEYKFNTNINGVSTDNGGLYIEPRGTFYTYERTPQQSIFSLEELFRHEYTHYLQARYLVDGLWGQGPFYEKNRLTWFDEGTAEFFAGSTRTSGVLPRKSILGYLAKDKVDHRYSLKKTLNSGYDDSDWMFYNYGFAVAHYLYEKDMPTFIKMNKAILNTDVKSYDEIIKKLSDDANKNTEYQNHIQELADKYQGAGIPLVSDDYLKDHGYKKASEVYSEISKAASLTNTSVTAEKSQYFNTFTLRGTYTGETSKGEFKDWDEMSKKLDGTLESLAKNSWSGYKTLTAYFTNYRVTSDNKVQYDVVFHGVLTDNA 790
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh..hhhhhhhhhhh.hhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhhhhhhh........hhhhheeeeee.hhhhhhhhhhhhh.......eeehhh.eeeee.........hhhhhhhhhhhhhhhhhhh.......hhhhh...hhhhhhhhhhhhh..........hhhhhhhhh........hhhhhhh.--....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.....hhhhhhhhhhhhhh.eeeeeeeee....eeeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh...hhhhhhheeeeeeeee....eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y3u A 110 NLYFQGGTmYDFEYLNGLSYTELTNLIKNIKWNQINGLFNYSTGSQKFFGDKNRVQAIINALQESGRTYTANDmKGIETFTEVLRAGFYLGYYNDGLSYLNDRNFQDKCIPAmIAIQKNPNFKLGTAVQDEVITSLGKLIGNASANAEVVNNCVPVLKQFRENLNQYAPDYVKGTAVNELIKGIEFDFSGAAYEKDVKTmPWYGKIDPFINELKALGLYGNITSATEWASDVGIYYLSKFGLYSTNRNDIVQSLEKAVDmYKYGKIAFVAmERITWDYDGIGSNGKKVDHDKFLDDAEKHYLPKTYTFDNGTFIIRAGDKVSEEKIKRLYWASREVKSQFHRVVGNDKALEVGNADDVLTmKIFNSPEEYKFNTNINGVSTDNGGLYIEPRGTFYTYERTPQQSIFSLEELFRHEYTHYLQARYLVDGLWGQGPFYEKNRLTWFDEGTAEFFAGSTRTSGVLPRKLILGYLAKDKVDHRYSLKKTLNS--DDSDWmFYNYGFAVAHYLYEKDmPTFIKmNKAILNTDVKSYDEIIKKLSDDANKNTEYQNHIQELVDKYQGAGIPLVSDDYLKDHGYKKASEVYSEISKAASLTNTSVTAEKSQYFNTFTLRGTYTGETSKGEFKDWDEmSKKLDGTLESLAKNSWSGYKTLTAYFTNYRVTSDNKVQYDVVFHGVLTDNG 790
                                   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       | -|    | 609       619  |    629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789 
                                  118-MSE                                                          183-MSE                                222-MSE                                                                                309-MSE                                                     369-MSE    380-MSE                                                                                   470-MSE                                                                                                                        597  |    |              622-MSE |                                                                                                            739-MSE                                               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    600    |                    628-MSE                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         605-MSE
   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 2Y3U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y3U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y3U)

(-) 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: 2y50 2y6i 2y72 4aqo 4are 4hpk 4jrw 4tn9 5iku

(-) Related Entries Specified in the PDB File

2y50 CRYSTAL STRUCTURE OF COLLAGENASE G FROM CLOSTRIDIUM HISTOLYTICUM AT 2.80 ANGSTROM RESOLUTION