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(-) Description

Title :  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.
 
Authors :  U. Eckhard, H. Brandstetter
Date :  21 Apr 12  (Deposition) - 05 Jun 13  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Hydrolase-Inhibitor Complex, Collagenolysis, Metalloprotease, Peptidase, Hydrolase (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
    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
 
Molecule 2 - ISOAMYL-PHOSPHONYL-GLY-PRO-ALA
    Chains: C, D
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2IP82Mod. Amino AcidISOPENTENYL PHOSPHATE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2IP81Mod. Amino AcidISOPENTENYL PHOSPHATE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2IP81Mod. Amino AcidISOPENTENYL PHOSPHATE
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:465 , HIS A:469 , GLU A:499 , IP8 C:0BINDING SITE FOR RESIDUE ZN A1731
2AC2SOFTWAREGLU A:440 , GLY A:473 , ILE A:477 , GLY A:479 , HOH A:2036 , HOH A:2055BINDING SITE FOR RESIDUE CA A1732
3AC3SOFTWAREHIS B:465 , HIS B:469 , GLU B:499 , IP8 D:0BINDING SITE FOR RESIDUE ZN B1731
4AC4SOFTWAREGLU B:440 , GLY B:473 , ILE B:477 , GLY B:479 , HOH B:2027 , HOH B:2045BINDING SITE FOR RESIDUE CA B1732
5AC5SOFTWAREGLY A:435 , GLY A:436 , SER A:455 , TYR A:457 , LEU A:462 , HIS A:465 , GLU A:466 , HIS A:469 , GLU A:499 , GLU A:503 , TRP A:545 , TYR A:548 , ZN A:1731 , HOH A:2050 , HOH A:2051 , HOH A:2056BINDING SITE FOR CHAIN C OF ISOAMYL-PHOSPHONYL-GLY-PRO-ALA
6AC6SOFTWAREASN B:434 , GLY B:435 , GLY B:436 , ILE B:437 , TYR B:438 , SER B:455 , TYR B:457 , LEU B:462 , HIS B:465 , GLU B:466 , HIS B:469 , GLU B:499 , GLU B:503 , TRP B:545 , TYR B:548 , ZN B:1731 , HOH B:2048BINDING SITE FOR CHAIN D OF ISOAMYL-PHOSPHONYL-GLY-PRO-ALA

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AR8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AR8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AR8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AR8)

(-) Exons   (0, 0)

(no "Exon" information available for 4AR8)

(-) 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:391
 aligned with Q899Y1_CLOTE | Q899Y1 from UniProtKB/TrEMBL  Length:991

    Alignment length:391
                                   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 
         Q899Y1_CLOTE   340 DINKLIEEGKKHYLPKTYTFDNGKIIIKAGDKVEESKIQKLYWASKEVKSQFHRIIGNDKPLEVGNADDILTIVIYNNPEEYKLNKTLYGYSVDNGGIYIEGIGTFFTYERTPQESIYSLEELFRHEFTHYLQGRYLIPGLFNKGDFYKGNNGRITWFEEGSAEFFAGSTRTSVLPRKSMVGGLSKNPKERFNADKLLHSKYSDGWDFYKYGYAFSDYMYNNNKKLFSDLVSTMKNNDVKGYEALIEESSKDSKINKDYEYHMENLVNNYDNYTIPLVSDDYMKQYDNKSLHEIKSDIEKAMDVKNSQITKESSQYFDTYNLKATYTLSSNKGEISNWNYMNNKINEALNKLDNLSWGGYKTVTAYFSNPRLNSNNEVVYDIVFHGLLSHN 730
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhhhhhhh........hhhhheeeeee.hhhhhhhhhhhh........eeehhh.eeeee.........hhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhh.........hhhhhhhh..hhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh......hhhhhhhhhhhhhh....eeeeee...eeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhheeeeeeeee.....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ar8 A 340 DINKLIEEGKKHYLPKTYTFDNGKIIIKAGDKVEESKIQKLYWASKEVKSQFHRIIGNDKPLEVGNADDILTIVIYNNPEEYKLNKTLYGYSVDNGGIYIEGIGTFFTYERTPQESIYSLEELFRHEFTHYLQGRYLIPGLFNKGDFYKGNNGRITWFEEGSAEFFAGSTRTSVLPRKSMVGGLSKNPKERFNADKLLHSKYSDGWDFYKYGYAFSDYMYNNNKKLFSDLVSTMKNNDVKGYEALIEESSKDSKINKDYEYHMENLVNNYDNYTIPLVSDDYMKQYDNKSLHEIKSDIEKAMDVKNSQITKESSQYFDTYNLKATYTLSSNKGEISNWNYMNNKINEALNKLDNLSWGGYKTVTAYFSNPRLNSNNEVVYDIVFHGLLSHN 730
                                   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 


Chain B from PDB  Type:PROTEIN  Length:389
 aligned with Q899Y1_CLOTE | Q899Y1 from UniProtKB/TrEMBL  Length:991

    Alignment length:389
                                   351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721         
         Q899Y1_CLOTE   342 NKLIEEGKKHYLPKTYTFDNGKIIIKAGDKVEESKIQKLYWASKEVKSQFHRIIGNDKPLEVGNADDILTIVIYNNPEEYKLNKTLYGYSVDNGGIYIEGIGTFFTYERTPQESIYSLEELFRHEFTHYLQGRYLIPGLFNKGDFYKGNNGRITWFEEGSAEFFAGSTRTSVLPRKSMVGGLSKNPKERFNADKLLHSKYSDGWDFYKYGYAFSDYMYNNNKKLFSDLVSTMKNNDVKGYEALIEESSKDSKINKDYEYHMENLVNNYDNYTIPLVSDDYMKQYDNKSLHEIKSDIEKAMDVKNSQITKESSQYFDTYNLKATYTLSSNKGEISNWNYMNNKINEALNKLDNLSWGGYKTVTAYFSNPRLNSNNEVVYDIVFHGLLSHN 730
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhhhhhhh........hhhhheeeeee.hhhhhhhhhhhh........eeehhh.eeeee.........hhhhhhhhhhhhhhhhhhh.......hhhhhh....hhhhhhhhhhhhh.........hhhhhhhh..hhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh......hhhhhhhhhhhhhh....eeeeee...eeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhheeeeeeeee.....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ar8 B 342 NKLIEEGKKHYLPKTYTFDNGKIIIKAGDKVEESKIQKLYWASKEVKSQFHRIIGNDKPLEVGNADDILTIVIYNNPEEYKLNKTLYGYSVDNGGIYIEGIGTFFTYERTPQESIYSLEELFRHEFTHYLQGRYLIPGLFNKGDFYKGNNGRITWFEEGSAEFFAGSTRTSVLPRKSMVGGLSKNPKERFNADKLLHSKYSDGWDFYKYGYAFSDYMYNNNKKLFSDLVSTMKNNDVKGYEALIEESSKDSKINKDYEYHMENLVNNYDNYTIPLVSDDYMKQYDNKSLHEIKSDIEKAMDVKNSQITKESSQYFDTYNLKATYTLSSNKGEISNWNYMNNKINEALNKLDNLSWGGYKTVTAYFSNPRLNSNNEVVYDIVFHGLLSHN 730
                                   351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721         


Chain C from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 4ar8 C   0 xGPA   3
                            |   
                            0-IP8


Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 4ar8 D   0 xGPA   3
                            |   
                            |   
                            0-IP8
   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 4AR8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AR8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AR8)

(-) 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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        Q899Y1_CLOTE | Q899Y1: 4ar9

(-) Related Entries Specified in the PDB File

4ar9 CRYSTAL STRUCTURE OF THE PEPTIDASE DOMAIN OF COLLAGENASE T FROM CLOSTRIDIUM TETANI AT 1.69 ANGSTROM RESOLUTION.