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(-) Description

Title :  CRYSTAL STRUCTURE OF A. NIGER OCHRATOXINASE
 
Authors :  D. Dobritzsch, H. Wang, G. Schneider, S. Yu
Date :  17 Sep 13  (Deposition) - 02 Jul 14  (Release) - 03 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Hydrolase, Metal-Dependent Amidohydrolase, Ochratoxin A Hydrolysis, Amidohydrolase Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Dobritzsch, H. Wang, G. Schneider, S. Yu
Structural And Functional Characterization Of Ochratoxinase, A Novel Mycotoxin Degrading Enzyme.
Biochem. J. V. 462 441 2014
PubMed-ID: 24947135  |  Reference-DOI: 10.1042/BJ20140382

(-) Compounds

Molecule 1 - OCHRATOXINASE
    Chains: A, B
    EC Number: 3.4.13.9, 3.5.1.-
    Engineered: YES
    Expression System: ASPERGILLUS NIGER
    Expression System Plasmid: PGAPT-OTASE
    Expression System Strain: AP4
    Expression System Taxid: 5061
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR, N-TERMINALLY TRUNCATED ISOFORM, RESIDUES 43-480
    Organism Scientific: ASPERGILLUS NIGER
    Organism Taxid: 5061
    Other Details: 42 RESIDUES TRUNCATED AT N-TERMINUS
    Strain: UVK143
    Synonym: PROLIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1KCX8Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:111 , HIS A:113 , KCX A:246 , ASP A:378 , ZN A:501BINDING SITE FOR RESIDUE ZN A 500
2AC2SOFTWAREHIS A:111 , KCX A:246 , HIS A:287 , HIS A:307 , ZN A:500BINDING SITE FOR RESIDUE ZN A 501
3AC3SOFTWAREHIS B:111 , HIS B:113 , KCX B:246 , ASP B:378 , ZN B:501BINDING SITE FOR RESIDUE ZN B 500
4AC4SOFTWAREHIS B:111 , KCX B:246 , HIS B:287 , HIS B:307 , ZN B:500BINDING SITE FOR RESIDUE ZN B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C5Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C5Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C5Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C5Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4C5Y)

(-) 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:436
 aligned with A2R2V4_ASPNC | A2R2V4 from UniProtKB/TrEMBL  Length:480

    Alignment length:436
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474      
         A2R2V4_ASPNC    45 DEAKVTIIYAGLLIPGDGEPLRNAALVISDKIIAFVGSEADIPKKYLRSTQSTHRVPVLMPGLWDCHMHFGGDDDYYNDYTSGLATHPASSGARLARGCWEALQNGYTSYRDLAGYGCEVAKAINDGTIVGPNVYSSGAALSQTAGHGDIFALPAGEVLGSYGVMNPRPGYWGAGPLCIADGVEEVRRAVRLQIRRGAKVIKVMASGGVMSRDDNPNFAQFSPEELKVIVEEAARQNRIVSAHVHGKAGIMAAIKAGCKSLEHVSYADEEVWELMKEKGILYVATRSVIEIFLASNGEGLVKESWAKLQALADSHLKAYQGAIKAGVTIALGTDTAPGGPTALELQFAVERGGMTPLEAIKAATANAPLSVGPQAPLTGQLREGYEADVIALEENPLEDIKVFQEPKAVTHVWKGGKLFKGPGIGPWGEDARNPFL 480
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.......eeeeeeeee..eeeeeee.hhhhhhhhhhh..eeeeeeeee.eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhh......eeee...eee...........hhhhhhhhhh.............eee..hhhhhhhhhhhhhhh....eeee.................hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh..eeee....hhhhhhhhhhhh.eee..hhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhhh...ee..........hhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhh.............eeee......hhhhhhhhh.eeeeee..eeee................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c5y A  45 DEAKVTIIYAGLLIPGDGEPLRNAALVISDKIIAFVGSEADIPKKYLRSTQSTHRVPVLMPGLWDCHMHFGGDDDYYNDYTSGLATHPASSGARLARGCWEALQNGYTSYRDLAGYGCEVAKAINDGTIVGPNVYSSGAALSQTAGHGDIFALPAGEVLGSYGVMNPRPGYWGAGPLCIADGVEEVRRAVRLQIRRGAKVIkVMASGGVMSRDDNPNFAQFSPEELKVIVEEAARQNRIVSAHVHGKAGIMAAIKAGCKSLEHVSYADEEVWELMKEKGILYVATRSVIEIFLASNGEGLVKESWAKLQALADSHLKAYQGAIKAGVTIALGTDTAPGGPTALELQFAVERGGMTPLEAIKAATANAPLSVGPQAPLTGQLREGYEADVIALEENPLEDIKVFQEPKAVTHVWKGGKLFKGPGIGPWGEDARNPFL 480
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244 |     254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474      
                                                                                                                                                                                                                                   246-KCX                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:433
 aligned with A2R2V4_ASPNC | A2R2V4 from UniProtKB/TrEMBL  Length:480

    Alignment length:436
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474      
         A2R2V4_ASPNC    45 DEAKVTIIYAGLLIPGDGEPLRNAALVISDKIIAFVGSEADIPKKYLRSTQSTHRVPVLMPGLWDCHMHFGGDDDYYNDYTSGLATHPASSGARLARGCWEALQNGYTSYRDLAGYGCEVAKAINDGTIVGPNVYSSGAALSQTAGHGDIFALPAGEVLGSYGVMNPRPGYWGAGPLCIADGVEEVRRAVRLQIRRGAKVIKVMASGGVMSRDDNPNFAQFSPEELKVIVEEAARQNRIVSAHVHGKAGIMAAIKAGCKSLEHVSYADEEVWELMKEKGILYVATRSVIEIFLASNGEGLVKESWAKLQALADSHLKAYQGAIKAGVTIALGTDTAPGGPTALELQFAVERGGMTPLEAIKAATANAPLSVGPQAPLTGQLREGYEADVIALEENPLEDIKVFQEPKAVTHVWKGGKLFKGPGIGPWGEDARNPFL 480
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.......eeeeeeeee..eeeeeee.hhhhhhhhhhh..eeeeeeeee.eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhh......eeee...eee...........hhhhhhhhhh.............eee..hhhhhhhhhhhhhhh....eeee.................hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh..eeee....hhhhhhhhhhhh.eee..hhhhhhhhhhh........---hhhhhhhhhhhhhhhhhh...ee..........hhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhh.............eeee......hhhhhhhhh.eeeeee..eeee................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c5y B  45 DEAKVTIIYAGLLIPGDGEPLRNAALVISDKIIAFVGSEADIPKKYLRSTQSTHRVPVLMPGLWDCHMHFGGDDDYYNDYTSGLATHPASSGARLARGCWEALQNGYTSYRDLAGYGCEVAKAINDGTIVGPNVYSSGAALSQTAGHGDIFALPAGEVLGSYGVMNPRPGYWGAGPLCIADGVEEVRRAVRLQIRRGAKVIkVMASGGVMSRDDNPNFAQFSPEELKVIVEEAARQNRIVSAHVHGKAGIMAAIKAGCKSLEHVSYADEEVWELMKEKGILYVATRSVIEIFLASNGEGLVKES---LQALADSHLKAYQGAIKAGVTIALGTDTAPGGPTALELQFAVERGGMTPLEAIKAATANAPLSVGPQAPLTGQLREGYEADVIALEENPLEDIKVFQEPKAVTHVWKGGKLFKGPGIGPWGEDARNPFL 480
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244 |     254       264       274       284       294       304       314       324       334       344   |   354       364       374       384       394       404       414       424       434       444       454       464       474      
                                                                                                                                                                                                                                   246-KCX                                                                                               348 352
   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 4C5Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C5Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C5Y)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A2R2V4_ASPNC | A2R2V4)
molecular function
    GO:0016805    dipeptidase activity    Catalysis of the hydrolysis of a dipeptide.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0102009    proline dipeptidase activity    Catalysis of the reaction: H2O + a dipeptide with proline at the C-terminal <=> L-proline + a standard alpha amino acid.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:1900817    ochratoxin A catabolic process    The chemical reactions and pathways resulting in the breakdown of ochratoxin A.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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 Related Entries

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

UniProtKB/Swiss-Prot
        A2R2V4_ASPNC | A2R2V4: 4c5z
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        A2R2V4_ASPNC | A2R2V4: 4c60 4c65

(-) Related Entries Specified in the PDB File

4c5z CRYSTAL STRUCTURE OF A. NIGER OCHRATOXINASE
4c60 CRYSTAL STRUCTURE OF A. NIGER OCHRATOXINASE
4c65 CRYSTAL STRUCTURE OF A. NIGER OCHRATOXINASE