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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA DJ-1D WITH GLYOXYLATE AS SUBSTRATE ANALOG
 
Authors :  D. Choi, J. Kim, K. -S. Ryu, C. Park
Date :  16 Jan 14  (Deposition) - 15 Oct 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Glyoxalase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Choi, J. Kim, S. Ha, K. Kwon, E. H. Kim, H. Y. Lee, K. S. Ryu, C. Park
Stereospecific Mechanism Of Dj-1 Glyoxalases Inferred From Their Hemithioacetal-Containing Crystal Structures.
Febs J. V. 281 5447 2014
PubMed-ID: 25283443  |  Reference-DOI: 10.1111/FEBS.13085

(-) Compounds

Molecule 1 - PROTEIN DJ-1 HOMOLOG D
    ChainsA, B, C
    EC Number4.2.1.130
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneDJ1D, AT3G02720, F13E7.34
    Organism CommonMOUSE-EAR CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymATDJ1D, LACTOYLGLUTATHIONE LYASE DJ1D

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1CGV6Mod. Amino AcidS-[(R)-CARBOXY(HYDROXY)METHYL]-L-CYSTEINE

(-) Sites  (0, 0)

(no "Site" information available for 4OGG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:351 -Pro A:352
2Asp B:351 -Pro B:352
3Asp C:351 -Pro C:352

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OGG)

(-) Sequences/Alignments

Asymmetric/Biological 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:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eehhhhhhhhhhhhhh..eeeee........ee.eeeee.......eeee...ee...hhhhhhhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhh......ee..hhhhhhhhhhh..ee........eeee..eeee.hhhhhhhhhhhhhhhh..eee....eeeee....eehhhhhhhhhhhhhhh.eeeee........ee.eeeee.......eeee...ee........hhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhhh.....ee..hhhhhhhhhhh..ee.........eee..eeee.hhhhhhhhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogg A   3 NSRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFESRGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASIcHGQLILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQLFVKALGGKITGANKRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGDRCPTAIHDFEGDQTYSEKPGHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASIcHGQQILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFVSQLMALLGIQVSF 388
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312|      322       332       342       352       362       372       382      
                                                                                                                                               120-CGV                                                                                                                                                                                          313-CGV                                                                       

Chain B from PDB  Type:PROTEIN  Length:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eehhhhhhhhhhhhhh..eeeee........ee.eeeee.......eeee...ee...hhhhhhhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhhh..eeee..hhhhhhhh......ee..hhhhhhhhhhh..ee........eeee..eeee.hhhhhhhhhhhhhhhh.eeee....eeeee....eehhhhhhhhhhhhhhh.eeeee........ee.eeeee.......eeee...ee...hhhhhhhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhhh..eeee..hhhhhhhh......ee..hhhhhhhhhhhh.ee.........eee..eeee.hhhhhhhhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogg B   3 NSRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFESRGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASIcHGQLILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQLFVKALGGKITGANKRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGDRCPTAIHDFEGDQTYSEKPGHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASIcHGQQILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFVSQLMALLGIQVSFH 389
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312|      322       332       342       352       362       372       382       
                                                                                                                                               120-CGV                                                                                                                                                                                          313-CGV                                                                        

Chain C from PDB  Type:PROTEIN  Length:388
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eehhhhhhhhhhhhhh.eeeeee........ee.eeeee.......eeee...ee...hhhhhhhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhhh..eeee..hhhhhhhh......ee..hhhhhhhhhhh..ee........eeee..eeee.hhhhhhhhhhhhhhhh.eeee....eeeee....eehhhhhhhhhhhhhhh.eeeee........ee.eeeee.......eeee...ee........hhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhhh.....ee..hhhhhhhhhhh..ee.........eee..eeee.hhhhhhhhhhhhhhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogg C   3 NSRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFESRGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASIcHGQLILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQLFVKALGGKITGANKRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGDRCPTAIHDFEGDQTYSEKPGHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASIcHGQQILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFVSQLMALLGIQVSFHH 390
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312|      322       332       342       352       362       372       382        
                                                                                                                                               120-CGV                                                                                                                                                                                          313-CGV                                                                         

   Legend:   → Mismatch (orange background)
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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 4OGG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:351 - Pro A:352   [ RasMol ]  
    Asp B:351 - Pro B:352   [ RasMol ]  
    Asp C:351 - Pro C:352   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        DJ1D_ARATH | Q9M8R43uk7 4ofw

(-) Related Entries Specified in the PDB File

4ofw 4ogf