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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF TARTRONATE SEMIALDEHYDE REDUCTASE [SALMONELLA TYPHIMURIUM LT2]
 
Authors :  J. Osipiuk, M. Zhou, S. Moy, F. Collart, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  22 Oct 04  (Deposition) - 26 Oct 04  (Release) - 06 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Mcsg, Protein Structure Initiative, Reductase, Tartronate, Psi, Midwest Center For Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, M. Zhou, S. Moy, F. Collart, A. Joachimiak
X-Ray Crystal Structure Of Garr-Tartronate Semialdehyde Reductase From Salmonella Typhimurium.
J Struct Funct Genomics V. 10 249 2009
PubMed-ID: 19184529  |  Reference-DOI: 10.1007/S10969-009-9059-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TARTRONATE SEMIALDEHYDE REDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GARR
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE15Mod. Amino AcidSELENOMETHIONINE
3TLA1Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:69 , ILE A:98 , ALA A:99 , ASN A:244BINDING SITE FOR RESIDUE CL A 502
2AC2SOFTWAREMSE A:13 , SER A:123 , GLY A:124 , GLY A:125 , LYS A:172 , ASN A:175 , GLN A:176 , LEU A:211 , PHE A:233 , HIS A:279 , HOH A:503 , HOH A:567 , HOH A:681BINDING SITE FOR RESIDUE TLA A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VPD)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:231 -Gly A:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VPD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VPD)

(-) Exons   (0, 0)

(no "Exon" information available for 1VPD)

(-) 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:294
 aligned with Q8ZLV8_SALTY | Q8ZLV8 from UniProtKB/TrEMBL  Length:296

    Alignment length:294
                                    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    
         Q8ZLV8_SALTY     3 MKVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVIITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAPVSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVALNIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSALACYYEKLAKVEVTR 296
               SCOP domains d1vpda2 A:3-163 Hydroxyisobutyrate dehydrogenase                                                                                                                 d1vpda1 A:164-296 Hydroxyisobutyrate dehydrogenase                                                                                    SCOP domains
               CATH domains -1vpdA01 A:4-165 NAD(P)-binding Rossmann-like Domain                                                                                                               1vpdA02 A:166-296 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                         CATH domains
               Pfam domains NAD_binding_2-1vpdA01 A:3-164                                                                                                                                     ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee..hhhhhhhhh.eeee...hhhhhhhhhhh..hhhhhh....eeee....hhhhhhhhhhhhhh...eeee..eehhhhhhhh..eeeeee.hhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vpd A   3 mKVGFIGLGImGKPmSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVIITmLPNSPHVKEVALGENGIIEGAKPGTVLIDmSSIAPLASREISDALKAKGVEmLDAPVSGGEPKAIDGTLSVmVGGDKAIFDKYYDLmKAmAGSVVHTGDIGAGNVTKLANQVIVALNIAAmSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPmVmDRNFKPGFRIDLHIKDLANALDTSHGVGAQLPLTAAVmEmmQALRADGHGNDDHSALACYYEKLAKVEVTR 296
                            |       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    
                            |        13-MSE                                              65-MSE                        95-MSE               117-MSE             137-MSE        152-MSE                           186-MSE                              223-MSE                                 263-MSE                             
                            3-MSE        17-MSE                                                                                                                                   155-MSE                                                               225-MSE                                 265-MSE                           
                                                                                                                                                                                                                                                                                                 266-MSE
   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  (2, 2)

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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8ZLV8_SALTY | Q8ZLV8)
molecular function
    GO:0008679    2-hydroxy-3-oxopropionate reductase activity    Catalysis of the reaction: (R)-glycerate + NADP+ = 2-hydroxy-3-oxopropanoate + NADPH + H+.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004616    phosphogluconate dehydrogenase (decarboxylating) activity    Catalysis of the reaction: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH + H+.
biological process
    GO:0046392    galactarate catabolic process    The chemical reactions and pathways resulting in the breakdown of galactarate, the anion of galactaric acid.
    GO:0046487    glyoxylate metabolic process    The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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