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(-) Description

Title :  SUBSTRATE PEPTIDE-BOUND STRUCTURE OF METALLOPROTEASE ZMP1 VARIANT E143AY178F FROM CLOSTRIDIUM DIFFICILE
 
Authors :  M. Schacherl, C. Pichlo, I. Neundorf, U. Baumann
Date :  23 Apr 15  (Deposition) - 05 Aug 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Hydrolase, Metalloprotease, Proline Specificity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Schacherl, C. Pichlo, I. Neundorf, U. Baumann
Structural Basis Of Proline-Proline Peptide Bond Specificity Of The Metalloprotease Zmp1 Implicated In Motility Of Clostridium Difficile.
Structure V. 23 1632 2015
PubMed-ID: 26211609  |  Reference-DOI: 10.1016/J.STR.2015.06.018

(-) Compounds

Molecule 1 - ZINC METALLOPROTEASE ZMP1
    Chains: A, B
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector: PET28A
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 272563
    Other Details: WITHOUT SIGNAL PEPTIDE (MISSING AA 1-26), CLEAVED N-TERMINAL HIS-TAG WITH THROMBIN, RESULTING GSH- OVERHANG
    Strain: 630
 
Molecule 2 - SUBSTRATE PEPTIDE
    Chains: C, D
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    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
1ACE2Mod. Amino AcidACETYL GROUP
2NH22Mod. Amino AcidAMINO GROUP
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2NH21Mod. Amino AcidAMINO GROUP
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2NH21Mod. Amino AcidAMINO GROUP
3ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:142 , HIS A:146 , GLU A:185 , PRO C:4BINDING SITE FOR RESIDUE ZN A1221
2AC2SOFTWAREHIS B:142 , HIS B:146 , GLU B:185 , PRO D:4BINDING SITE FOR RESIDUE ZN B1221

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A0X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A0X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A0X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A0X)

(-) Exons   (0, 0)

(no "Exon" information available for 5A0X)

(-) 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:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..ee......hhhhhhhhhhhhh..hhhhhhhhhhh...eeee..hhhhhhhhhhhh............hhhhh.eeee..eeee.............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a0x A  27 DSTTIQQNKDTLSQIVVFPTGNYDKNEANAMVNRLANIDGKYLNALKQNNLKIKLLSGKLTDEKEYAYLKGVVPKGWEGTGKTWDDVPGLGGSTVALRIGFSNKGKGHDAINLELHATAHAIDHIVLNDISKSAQFKQIFAKEGRSLGNVNFLGVYPEEFFAESFAYYYLNQDTNSKLKSACPQTYSFLQNLAK 220
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216    


Chain B from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.ee......hhhhhhhhhhhhh..hhhhhhhhhhh...eeee..hhhhhhhhhhhh............hhhhh.eeee..eeee.............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a0x B  30 TIQQNKDTLSQIVVFPTGNYDKNEANAMVNRLANIDGKYLNALKQNNLKIKLLSGKLTDEKEYAYLKGVVPKGWEGTGKTWDDVPGLGGSTVALRIGFSNKGKGHDAINLELHATAHAIDHIVLNDISKSAQFKQIFAKEGRSLGNVNFLGVYPEEFFAESFAYYYLNQDTNSKLKSACPQTYSFLQNLAK 220
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 


Chain C from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..ee..... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 5a0x C   0 xEVNPPVPx   8
                            |       |
                            0-ACE   8-NH2


Chain D from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..ee..... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 5a0x D   0 xEVNPPVPx   8
                            |       |
                            |       8-NH2
                            0-ACE
   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 5A0X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A0X)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (7, 7)

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 Related Entries

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UniProtKB/Swiss-Prot
        ZMP1_PEPD6 | Q183R7: 2n6j 5a0p 5a0r 5a0s

(-) Related Entries Specified in the PDB File

5a0p APO-STRUCTURE OF METALLOPROTEASE ZMP1 FROM CLOSTRIDIUM DIFFICILE
5a0r PRODUCT PEPTIDE-BOUND STRUCTURE OF METALLOPROTEASE ZMP1 VARIANT E143A FROM CLOSTRIDIUM DIFFICILE
5a0s APO-STRUCTURE OF METALLOPROTEASE ZMP1 VARIANT E143A FROM CLOSTRIDIUM DIFFICILE