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(-) Description

Title :  CRYSTAL STRUCTURE OF CLOSTRIDIUM HISTOLYTICUM COLG COLLAGENASE COLLAGEN-BINDING DOMAIN 3B AT 1.0 ANGSTROM RESOLUTION IN ABSENCE OF CALCIUM
 
Authors :  J. J. Wilson, O. Matsushita, A. Okabe, J. Sakon
Date :  21 Jan 03  (Deposition) - 15 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Sandwich, Metalloprotease, Collagen-Binding Domain, Lithium, Chlorine, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Wilson, O. Matsushita, A. Okabe, J. Sakon
A Bacterial Collagen-Binding Domain With Novel Calcium-Binding Motif Controls Domain Orientation
Embo J. V. 22 1743 2003
PubMed-ID: 12682007  |  Reference-DOI: 10.1093/EMBOJ/CDG172
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLASS 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
    Gene: COLG
    Organism Scientific: CLOSTRIDIUM HISTOLYTICUM
    Organism Taxid: 1498

 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
1CL2Ligand/IonCHLORIDE ION
2LI3Ligand/IonLITHIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2LI-1Ligand/IonLITHIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2LI-1Ligand/IonLITHIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:937 , GLU A:938 , LYS A:1008BINDING SITE FOR RESIDUE CL A 1009
2AC2SOFTWARESER A:922 , ASP A:927 , ASP A:930 , HOH A:2106BINDING SITE FOR RESIDUE LI A 1010
3AC3SOFTWARELYS B:937 , GLU B:938 , LYS B:1008BINDING SITE FOR RESIDUE CL B 1009
4AC4SOFTWAREASP B:927 , ARG B:929 , ASP B:930 , LI B:1011 , HOH B:2051BINDING SITE FOR RESIDUE LI B 1010
5AC5SOFTWARESER B:922 , ASP B:927 , ASP B:930 , LI B:1010 , HOH B:2285BINDING SITE FOR RESIDUE LI B 1011

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NQJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NQJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NQJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NQJ)

(-) Exons   (0, 0)

(no "Exon" information available for 1NQJ)

(-) 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:98
 aligned with Q9S0X0_HATHI | Q9S0X0 from UniProtKB/TrEMBL  Length:1118

    Alignment length:101
                                  1027      1037      1047      1057      1067      1077      1087      1097      1107      1117 
        Q9S0X0_HATHI   1018 KATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 1118
               SCOP domains d1nqja_ A: Class 1 collagenase                                                                        SCOP domains
               CATH domains 1nqjA00 A:908-1008  [code=2.60.120.380, no name defined   ]                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.......eeeee.....eeeeeeee...eeeeeeeee....eeeeeeee..---...ee.eee..eeeeeeee..eeeeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                1nqj A  908 KATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPES---DRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 1008
                                   917       927       937       947       957    |  967       977       987       997      1007 
                                                                                962 966                                          


Chain B from PDB  Type:PROTEIN  Length:115
 aligned with Q9S0X0_HATHI | Q9S0X0 from UniProtKB/TrEMBL  Length:1118

    Alignment length:115
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113     
        Q9S0X0_HATHI   1004 NEKLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 1118
               SCOP domains d1nqjb_ B: Class 1 collagenase                                                                                      SCOP domains
               CATH domains 1nqjB00 B:894-1008  [code=2.60.120.380, no name defined]                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhee.......eeeee.....eeeeeeee...eeeeeeeee....eeeeeeee........ee.eee..eeeeeeee..eeeeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                1nqj B  894 NEKLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK 1008
                                   903       913       923       933       943       953       963       973       983       993      1003
   Legend:   → Mismatch (orange background)
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  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 1NQJ)

(-) Gene Ontology  (5, 5)

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.

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  1nqj
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  3.4.24.3
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 Related Entries

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

UniProtKB/TrEMBL
        Q9S0X0_HATHI | Q9S0X0: 1nqd 2o8o

(-) Related Entries Specified in the PDB File

1nqd THE SAME PROTEIN WITH CALCIUM IONS BOUND.