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(-) Description

Title :  STRUCTURE OF MALEYL PYRUVATE ISOMERASE, A BACTERIAL GLUTATHIONE-S-TRANSFERASE IN ZETA CLASS, IN COMPLEX WITH SUBSTRATE ANALOGUE DICARBOXYETHYL GLUTATHIONE
 
Authors :  D. K. Shoemark, N. -Y. Zhou, P. A. Williams, A. T. Hadfield
Date :  19 Jul 07  (Deposition) - 22 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glutathione-S-Transferase, Gst, Plasmid, Pyruvate, Bacterial, Isomerase, Biodegradation, Maleyl Pyruvate, Fumaryl Pyruvate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Marsh, D. K. Shoemark, A. Jacob, C. Robinson, B. Cahill, N. -Y. Zhou, P. A. Williams, A. T. Hadfield
Structure Of Bacterial Glutathione-S-Transferase Maleyl Pyruvate Isomerase And Implications For Mechanism Of Isomerisation.
J. Mol. Biol. V. 384 165 2008
PubMed-ID: 18824004  |  Reference-DOI: 10.1016/J.JMB.2008.09.028
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MALEYLPYRUVATE ISOMERASE
    Chains: A, B
    EC Number: 5.2.1.2
    Engineered: YES
    Expression System: ESCHERICIA COLI
    Expression System Plasmid: PET 28
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Organism Scientific: RALSTONIA SP.
    Organism Taxid: 70356
    Strain: U2
    Synonym: MALEYL PYRUVATE ISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2NA2Ligand/IonSODIUM ION
3TGG2Ligand/IonGAMMA-GLUTAMYL-S-(1,2-DICARBOXYETHYL)CYSTEINYLGLYCINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:9 , GLY A:10 , THR A:11 , ARG A:14 , LEU A:33 , HIS A:38 , LEU A:51 , VAL A:52 , GLN A:64 , SER A:65 , PRO A:66 , HIS A:104 , ASN A:108 , ARG A:109 , ARG A:110 , ARG A:176 , HOH A:2010 , HOH A:2221 , HOH A:2360 , HOH A:2361 , HOH A:2362 , HOH A:2363 , HOH A:2364 , HOH A:2365 , CYS B:101 , ASP B:102 , HOH B:2190BINDING SITE FOR RESIDUE TGG A1213
2AC2SOFTWARECYS A:101 , ASP A:102 , HOH A:2216 , SER B:9 , GLY B:10 , THR B:11 , ARG B:14 , LEU B:33 , HIS B:38 , LEU B:51 , VAL B:52 , GLN B:64 , SER B:65 , PRO B:66 , HIS B:104 , ASN B:108 , ARG B:109 , ARG B:110 , ARG B:176 , HOH B:2011 , HOH B:2194 , HOH B:2196 , HOH B:2285 , HOH B:2343 , HOH B:2344 , HOH B:2345 , HOH B:2346 , HOH B:2347 , HOH B:2348BINDING SITE FOR RESIDUE TGG B1213
3AC3SOFTWAREARG A:175 , HOH A:2139 , HOH A:2141 , HOH A:2325BINDING SITE FOR RESIDUE NA A1214
4AC4SOFTWAREARG B:175 , HOH B:2133 , HOH B:2284 , HOH B:2309BINDING SITE FOR RESIDUE NA B1214
5AC5SOFTWAREARG A:109 , GLU A:113 , ARG A:116 , HOH A:2366 , HOH A:2367BINDING SITE FOR RESIDUE ACT A1215
6AC6SOFTWAREARG B:109 , GLU B:113 , ARG B:116 , HOH B:2349 , HOH B:2350BINDING SITE FOR RESIDUE ACT B1215

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V6K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V6K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V6K)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_NTERPS50404 Soluble glutathione S-transferase N-terminal domain profile.NAGL_RALSP1-80
 		  2A:1-80
B:1-80
2GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.NAGL_RALSP85-212
 		  2A:85-212
B:85-212

(-) Exons   (0, 0)

(no "Exon" information available for 2V6K)

(-) 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:214
 aligned with NAGL_RALSP | O86043 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:214
                              1                                                                                                                                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    
           NAGL_RALSP     - --MKLYNFWRSGTSHRLRIALNLKGVPYEYLAVHLGKEEHLKDAFKALNPQQLVPALDTGAQVLIQSPAIIEWLEEQYPTPALLPADADGRQRVRALAAIVGCDIHPINNRRILEYLRKTFGADEAAINAWCGTWISAGFDAYEALLAVDPKRGRYSFGDTPTLADCYLVPQVESARRFQVDLTPYPLIRAVDAACGELDAFRRAAPAAQPDSA 212
               SCOP domains d2v6ka1 A:-1-79 automated matches                                                d2v6ka2 A:80-212 automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------2v6kA02 A:83-212  [code=1.20.1050.10, no name defined]                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh......eee....eeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GST_NTER  PDB: A:1-80 UniProt: 1-80                                             ----GST_CTER  PDB: A:85-212 UniProt: 85-212                                                                                          PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v6k A  -1 AKMKLYNFWRSGTSHRLRIALNLKGVPYEYLAVHLGKEEHLKDAFKALNPQQLVPALDTGAQVLIQSPAIIEWLEEQYPTPALLPADADGRQRVRALAAIVGCDIHPINNRRILEYLRKTFGADEAAINAWCGTWISAGFDAYEALLAVDPKRGRYSFGDTPTLADCYLVPQVESARRFQVDLTPYPLIRAVDAACGELDAFRRAAPAAQPDSA 212
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    


Chain B from PDB  Type:PROTEIN  Length:214
 aligned with NAGL_RALSP | O86043 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:214
                              1                                                                                                                                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    
           NAGL_RALSP     - --MKLYNFWRSGTSHRLRIALNLKGVPYEYLAVHLGKEEHLKDAFKALNPQQLVPALDTGAQVLIQSPAIIEWLEEQYPTPALLPADADGRQRVRALAAIVGCDIHPINNRRILEYLRKTFGADEAAINAWCGTWISAGFDAYEALLAVDPKRGRYSFGDTPTLADCYLVPQVESARRFQVDLTPYPLIRAVDAACGELDAFRRAAPAAQPDSA 212
               SCOP domains d2v6kb1 B:-1-79 automated matches                                                d2v6kb2 B:80-212 automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------2v6kB02 B:83-212  [code=1.20.1050.10, no name defined]                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh......eee....eeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GST_NTER  PDB: B:1-80 UniProt: 1-80                                             ----GST_CTER  PDB: B:85-212 UniProt: 85-212                                                                                          PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v6k B  -1 AKMKLYNFWRSGTSHRLRIALNLKGVPYEYLAVHLGKEEHLKDAFKALNPQQLVPALDTGAQVLIQSPAIIEWLEEQYPTPALLPADADGRQRVRALAAIVGCDIHPINNRRILEYLRKTFGADEAAINAWCGTWISAGFDAYEALLAVDPKRGRYSFGDTPTLADCYLVPQVESARRFQVDLTPYPLIRAVDAACGELDAFRRAAPAAQPDSA 212
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2V6K)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NAGL_RALSP | O86043)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0050077    maleylpyruvate isomerase activity    Catalysis of the reaction: 3-maleylpyruvate = 3-fumarylpyruvate.
biological process
    GO:0009072    aromatic amino acid family metabolic process    The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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        NAGL_RALSP | O86043: 2jl4

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