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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PEPTIDASE DOMAIN OF COLLAGENASE T FROM CLOSTRIDIUM TETANI AT 1.69 ANGSTROM RESOLUTION.
 
Authors :  U. Eckhard, H. Brandstetter
Date :  22 Apr 12  (Deposition) - 05 Jun 13  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Collagen, Metalloprotease, Peptidase, Collagenolysis (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

(-) Compounds

Molecule 1 - COLLAGENASE COLT
    Chains: A, B
    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: PEPTIDASE DOMAIN, RESIDUES 340-730
    Organism Scientific: CLOSTRIDIUM TETANI
    Organism Taxid: 1513
    Synonym: COLLAGENASE T

 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, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:465 , GLU A:466 , HIS A:469 , GLU A:499 , HOH A:2107 , HOH A:2108BINDING SITE FOR RESIDUE ZN A1731
2AC2SOFTWAREGLU A:440 , GLY A:473 , ILE A:477 , GLY A:479 , HOH A:2055 , HOH A:2089BINDING SITE FOR RESIDUE CA A1732
3AC3SOFTWAREHIS B:465 , HIS B:469 , GLU B:499 , HOH B:2093BINDING SITE FOR RESIDUE ZN B1731
4AC4SOFTWAREGLU B:440 , GLY B:473 , ILE B:477 , GLY B:479 , HOH B:2052 , HOH B:2082BINDING SITE FOR RESIDUE CA B1732

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AR9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AR9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AR9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AR9)

(-) Exons   (0, 0)

(no "Exon" information available for 4AR9)

(-) 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:392
 aligned with Q899Y1_CLOTE | Q899Y1 from UniProtKB/TrEMBL  Length:991

    Alignment length:392
                                   348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728  
         Q899Y1_CLOTE   339 IDINKLIEEGKKHYLPKTYTFDNGKIIIKAGDKVEESKIQKLYWASKEVKSQFHRIIGNDKPLEVGNADDILTIVIYNNPEEYKLNKTLYGYSVDNGGIYIEGIGTFFTYERTPQESIYSLEELFRHEFTHYLQGRYLIPGLFNKGDFYKGNNGRITWFEEGSAEFFAGSTRTSVLPRKSMVGGLSKNPKERFNADKLLHSKYSDGWDFYKYGYAFSDYMYNNNKKLFSDLVSTMKNNDVKGYEALIEESSKDSKINKDYEYHMENLVNNYDNYTIPLVSDDYMKQYDNKSLHEIKSDIEKAMDVKNSQITKESSQYFDTYNLKATYTLSSNKGEISNWNYMNNKINEALNKLDNLSWGGYKTVTAYFSNPRLNSNNEVVYDIVFHGLLSHN 730
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhhhhhhh........hhhhheeeeee.hhhhhhhhhhhh.......eeeehhh.eeeee.........hhhhhhhhhhhhhhhhhhh.......hhhhh.....hhhhhhhhhhhhh.........hhhhhh....hhhhh.hhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhhhhhhhhh....eeeeee...eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhheeeeeeeee.....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ar9 A 339 TDINKLIEEGKKHYLPKTYTFDNGKIIIKAGDKVEESKIQKLYWASKEVKSQFHRIIGNDKPLEVGNADDILTIVIYNNPEEYKLNKTLYGYSVDNGGIYIEGIGTFFTYERTPQESIYSLEELFRHEFTHYLQGRYLIPGLFNKGDFYKGNNGRITWFEEGSAEFFAGSTRTSVLPRKSMVGGLSKNPKERFNADKLLHSKYSDGWDFYKYGYAFSDYMYNNNKKLFSDLVSTMKNNDVKGYEALIEESSKDSKINKDYEYHMENLVNNYDNYTIPLVSDDYMKQYDNKSLHEIKSDIEKAMDVKNSQITKESSQYFDTYNLKATYTLSSNKGEISNWNYMNNKINEALNKLDNLSWGGYKTVTAYFSNPRLNSNNEVVYDIVFHGLLSHN 730
                                   348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728  


Chain B from PDB  Type:PROTEIN  Length:392
 aligned with Q899Y1_CLOTE | Q899Y1 from UniProtKB/TrEMBL  Length:991

    Alignment length:392
                                   348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728  
         Q899Y1_CLOTE   339 IDINKLIEEGKKHYLPKTYTFDNGKIIIKAGDKVEESKIQKLYWASKEVKSQFHRIIGNDKPLEVGNADDILTIVIYNNPEEYKLNKTLYGYSVDNGGIYIEGIGTFFTYERTPQESIYSLEELFRHEFTHYLQGRYLIPGLFNKGDFYKGNNGRITWFEEGSAEFFAGSTRTSVLPRKSMVGGLSKNPKERFNADKLLHSKYSDGWDFYKYGYAFSDYMYNNNKKLFSDLVSTMKNNDVKGYEALIEESSKDSKINKDYEYHMENLVNNYDNYTIPLVSDDYMKQYDNKSLHEIKSDIEKAMDVKNSQITKESSQYFDTYNLKATYTLSSNKGEISNWNYMNNKINEALNKLDNLSWGGYKTVTAYFSNPRLNSNNEVVYDIVFHGLLSHN 730
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhhhhhhh........hhhhheeeeee.hhhhhhhhhhhh.......eeeehhh.eeeee.........hhhhhhhhhhhhhhhhhhh.......hhhhh.....hhhhhhhhhhhhh.........hhhhhh....hhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh......hhhhhhhhhhhhhh....eeeeee...eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhheeeeeeeee.....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ar9 B 339 TDINKLIEEGKKHYLPKTYTFDNGKIIIKAGDKVEESKIQKLYWASKEVKSQFHRIIGNDKPLEVGNADDILTIVIYNNPEEYKLNKTLYGYSVDNGGIYIEGIGTFFTYERTPQESIYSLEELFRHEFTHYLQGRYLIPGLFNKGDFYKGNNGRITWFEEGSAEFFAGSTRTSVLPRKSMVGGLSKNPKERFNADKLLHSKYSDGWDFYKYGYAFSDYMYNNNKKLFSDLVSTMKNNDVKGYEALIEESSKDSKINKDYEYHMENLVNNYDNYTIPLVSDDYMKQYDNKSLHEIKSDIEKAMDVKNSQITKESSQYFDTYNLKATYTLSSNKGEISNWNYMNNKINEALNKLDNLSWGGYKTVTAYFSNPRLNSNNEVVYDIVFHGLLSHN 730
                                   348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728
   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 4AR9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AR9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AR9)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q899Y1_CLOTE | Q899Y1)
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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 Related Entries

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

UniProtKB/TrEMBL
        Q899Y1_CLOTE | Q899Y1: 4ar8

(-) Related Entries Specified in the PDB File

4ar8 CRYSTAL STRUCTURE OF THE PEPTIDASE DOMAIN OF COLLAGENASE T FROM CLOSTRIDIUM TETANI COMPLEXED WITH THE PEPTIDIC INHIBITOR ISOAMYL-PHOSPHONYL-GLY-PRO-ALA AT 2.05 ANGSTROM RESOLUTION.
4are CRYSTAL STRUCTURE OF THE COLLAGENASE UNIT OF COLLAGENASE G FROM CLOSTRIDIUM HISTOLYTICUM AT 2.19 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.