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(-) Description

Title :  CRYSTAL STRUCTURE OF CLOSTRIDIUM HISTOLYTICUM COLG COLLAGENASE COLLAGEN-BINDING DOMAIN 3B AT 1.35 ANGSTROM RESOLUTION IN PRESENCE OF CALCIUM
 
Authors :  S. T. L. Philominathan, J. J Wilson, O. Matsushita, J. Sakon
Date :  12 Dec 06  (Deposition) - 11 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Helix To Beta Transtition, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. T. L. Philominathan, J. J. Wilson, O. Matsushita, J. Sakon
Induction Of Stable Beta-Sheet By Ca2+ In Clostridial Collagen Binding Domain
To Be Published
PubMed: search
(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 BL21
    Expression System Plasmid: PGEX-4T-2
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: COLLAGEN-BINDING DOMAIN, RESIDUES 1003-1118
    Gene: COLG
    Organism Scientific: CLOSTRIDIUM HISTOLYTICUM
    Organism Taxid: 1498
    Strain: JCM1403

 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  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:1899 , GLU B:1901 , SER B:1922 , ASP B:1927 , ASP B:1930 , HOH B:3025BINDING SITE FOR RESIDUE CA B 2009
2AC2SOFTWAREGLU B:1901 , ASN B:1903 , ASP B:1904 , ASP B:1927 , ARG B:1929 , ASP B:1930BINDING SITE FOR RESIDUE CA B 2010
3AC3SOFTWAREGLU A:901 , ASN A:903 , ASP A:904 , ASP A:927 , ARG A:929 , ASP A:930BINDING SITE FOR RESIDUE CA A 1009
4AC4SOFTWAREGLU A:899 , GLU A:901 , SER A:922 , ASP A:927 , ASP A:930 , HOH A:3018BINDING SITE FOR RESIDUE CA A 1010
5AC5SOFTWARELYS A:937 , GLU A:938 , LYS A:1008BINDING SITE FOR RESIDUE CL A 1011

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O8O)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:901 -Asn A:902
2Glu B:1901 -Asn B:1902

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O8O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O8O)

(-) Exons   (0, 0)

(no "Exon" information available for 2O8O)

(-) 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:110
 aligned with Q9S0X0_HATHI | Q9S0X0 from UniProtKB/TrEMBL  Length:1118

    Alignment length:113
                                  1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115   
        Q9S0X0_HATHI   1006 KLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 1118
               SCOP domains d2o8oa_ A: Class 1 collagenase                                                                                    SCOP domains
               CATH domains 2o8oA00 A:896-1008  [code=2.60.120.380, no name defined]                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......hhhhhee.......eeeee.....eeeeeeee...eeeeeeeee....eeeeeeee..---...ee.eee..eeeeeeee..eeeeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                2o8o A  896 KLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPES---DRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 1008
                                   905       915       925       935       945       955      |  -|      975       985       995      1005   
                                                                                            962 966                                          


Chain A from PDB  Type:PROTEIN  Length:110
 aligned with Q9X721_HATHI | Q9X721 from UniProtKB/TrEMBL  Length:1118

    Alignment length:113
                                  1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115   
        Q9X721_HATHI   1006 KLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 1118
               SCOP domains d2o8oa_ A: Class 1 collagenase                                                                                    SCOP domains
               CATH domains 2o8oA00 A:896-1008  [code=2.60.120.380, no name defined]                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......hhhhhee.......eeeee.....eeeeeeee...eeeeeeeee....eeeeeeee..---...ee.eee..eeeeeeee..eeeeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                2o8o A  896 KLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPES---DRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 1008
                                   905       915       925       935       945       955      |  -|      975       985       995      1005   
                                                                                            962 966                                          


Chain B from PDB  Type:PROTEIN  Length:114
 aligned with Q9S0X0_HATHI | Q9S0X0 from UniProtKB/TrEMBL  Length:1118

    Alignment length:120
                                  1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118
        Q9S0X0_HATHI    999 IKGLGNEKLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 1118
               SCOP domains d2  o8ob_ B: Class 1 collagenase                                                                                         SCOP domains
               CATH domains 2o  8oB00 B:1891-2008  [code=2.60.120.380, no name defined]                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..--..eeee......hhhhhee.....eeeeeee.....eeeeeeee...eeeeeeeee....eeeeeeee..----..ee.eee..eeeeeeee..eeeeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                2o8o B 1891 IP--GNEKLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPES----RITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 2008
                             |  | 1898      1908      1918      1928      1938      1948      1958   |  1968      1978      1988      1998      2008
                          1892  |                                                                 1962 1967                                         
                             1893                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:114
 aligned with Q9X721_HATHI | Q9X721 from UniProtKB/TrEMBL  Length:1118

    Alignment length:120
                                  1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118
        Q9X721_HATHI    999 IKGLGNEKLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 1118
               SCOP domains d2  o8ob_ B: Class 1 collagenase                                                                                         SCOP domains
               CATH domains 2o  8oB00 B:1891-2008  [code=2.60.120.380, no name defined]                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..--..eeee......hhhhhee.....eeeeeee.....eeeeeeee...eeeeeeeee....eeeeeeee..----..ee.eee..eeeeeeee..eeeeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                2o8o B 1891 IP--GNEKLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPES----RITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 2008
                             |  | 1898      1908      1918      1928      1938      1948      1958   |  1968      1978      1988      1998      2008
                          1892  |                                                                 1962 1967                                         
                             1893
   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  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2O8O)

(-) Gene Ontology  (5, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9S0X0_HATHI | Q9S0X0)
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.

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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  2o8o
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 Related Entries

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

UniProtKB/TrEMBL
        Q9S0X0_HATHI | Q9S0X0: 1nqd 1nqj
        Q9X721_HATHI | Q9X721: 2y3u 2y50 2y6i 2y72 4aqo 4are 4hpk 4jrw 4tn9 5iku

(-) Related Entries Specified in the PDB File

1nqd A BACTERIAL COLLAGEN-BINDING DOMAIN WITH NOVEL CALCIUM- BINDING MOTIF
1nqj SAME PROTEIN IN THE ABSENCE OF CALCIUM