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(-) Description

Title :  PRODUCT PEPTIDE-BOUND STRUCTURE OF METALLOPROTEASE ZMP1 VARIANT E143A FROM CLOSTRIDIUM DIFFICILE
 
Authors :  M. Schacherl, C. Pichlo, I. Neundorf, U. Baumann
Date :  22 Apr 15  (Deposition) - 05 Aug 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Keywords :  Hydrolase, Metalloprotease, Zmp1, 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
    Synonym: ZMP1
 
Molecule 2 - PRODUCT PEPTIDE
    Chains: D, E
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): A D 
Biological Unit 2 (1x):  B E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2GOL4Ligand/IonGLYCEROL
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2GOL3Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2GOL1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:142 , HIS A:146 , GLU A:185 , PRO D:4BINDING SITE FOR RESIDUE ZN A1221
2AC2SOFTWAREHIS B:142 , HIS B:146 , GLU B:185 , PRO E:4BINDING SITE FOR RESIDUE ZN B1221
3AC3SOFTWAREGLY A:102 , THR A:106 , ASP A:135 , ASN A:175 , HOH A:2178 , HOH A:2181 , HOH A:2261 , ASN B:177BINDING SITE FOR RESIDUE GOL A1222
4AC4SOFTWAREASN A:48 , TYR A:49 , LYS A:51 , ILE A:156BINDING SITE FOR RESIDUE GOL A1223
5AC5SOFTWAREASN A:177 , GLY B:102 , ASP B:135 , ASN B:175 , HOH B:2129BINDING SITE FOR RESIDUE GOL B1222
6AC6SOFTWARELYS A:130 , HOH A:2217 , LYS B:130 , ASN B:175BINDING SITE FOR RESIDUE GOL A1224

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A0R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A0R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A0R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A0R)

(-) Exons   (0, 0)

(no "Exon" information available for 5A0R)

(-) 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:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh.ee......hhhhhhhhhhhhh..hhhhhhhhhhh...eeee..hhhhhhhhhhhh............hhhhh.eeee..eeee.............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5a0r A  29 TTIQQNKDTLSQIVVFPTGNYDKNEANAMVNRLANIDGKYLNALKQNNLKIKLLSGKLTDEKEYAYLKGVVPKGWEGTGKTWDDVPGLGGSTVALRIGFSNKGKGHDAINLELHATAHAIDHIVLNDISKSAQFKQIFAKEGRSLGNVNYLGVYPEEFFAESFAYYYLNQDTNSKLKSACPQTYSFLQNLAK 220
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218  


Chain B from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhee......hhhhhhhhhhhhh..hhhhhhhhhhh...eeee..hhhhhhhhhhhh............hhhhh.eeee..eeee.............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5a0r B  29 TTIQQNKDTLSQIVVFPTGNYDKNEANAMVNRLANIDGKYLNALKQNNLKIKLLSGKLTDEKEYAYLKGVVPKGWEGTGKTWDDVPGLGGSTVALRIGFSNKGKGHDAINLELHATAHAIDHIVLNDISKSAQFKQIFAKEGRSLGNVNYLGVYPEEFFAESFAYYYLNQDTNSKLKSACPQTYSFLQNLAK 220
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218  


Chain D from PDB  Type:PROTEIN  Length:5
                                     
               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
                 5a0r D   0 xEVNP   4
                            |    
                            0-ACE


Chain E from PDB  Type:PROTEIN  Length:5
                                     
               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
                 5a0r E   0 xEVNP   4
                            |    
                            |    
                            0-ACE
   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 5A0R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A0R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A0R)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        ZMP1_PEPD6 | Q183R7: 2n6j 5a0p 5a0s 5a0x

(-) Related Entries Specified in the PDB File

5a0p APO-STRUCTURE OF METALLOPROTEASE ZMP1 FROM CLOSTRIDIUM DIFFICILE
5a0s APO-STRUCTURE OF METALLOPROTEASE ZMP1 VARIANT E143A FROM CLOSTRIDIUM DIFFICILE
5a0x SUBSTRATE PEPTIDE-BOUND STRUCTURE OF METALLOPROTEASE ZMP1 VARIANT E143AY178F FROM CLOSTRIDIUM DIFFICILE