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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TARTRONIC SEMIALDEHYDE REDUCTASE FROM SALMONELLA TYPHIMURIUM LT2
 
Authors :  Y. Kim, R. Wu, F. Collart, A. Joachimiak, Midwest Center For Structu Genomics (Mcsg)
Date :  20 Dec 04  (Deposition) - 01 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Structural Genomics, Tartronic Semialdehyde Reductase, Oxidoreductase, Salmonella Typhimurium Lt2, Psi, Protein Structure Initiative, The Midwest Center For Structural Genomics, Mcsg (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

(-) Compounds

Molecule 1 - TARTRONIC SEMIALDEHYDE REDUCTASE
    Chains: A, B
    EC Number: 1.1.1.60
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID WITH T7 PROMOTER
    Fragment: TARTRONIC SEMIALDEHYDE REDUCTASE
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 22)

Asymmetric Unit (1, 22)
No.NameCountTypeFull Name
1MSE22Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 44)
No.NameCountTypeFull Name
1MSE44Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1YB4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YB4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YB4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YB4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YB4)

(-) Exons   (0, 0)

(no "Exon" information available for 1YB4)

(-) 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:291
 aligned with Q8ZR83_SALTY | Q8ZR83 from UniProtKB/TrEMBL  Length:292

    Alignment length:291
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
         Q8ZR83_SALTY     1 MKLGFIGLGIMGSPMAINLARAGHQLHVTTIGPVADELLSLGAVNVETARQVTEFADIIFIMVPDTPQVEDVLFGEHGCAKTSLQGKTIVDMSSISPIETKRFAQRVNEMGADYLDAPVSGGEIGAREGTLSIMVGGEQKVFDRVKPLFDILGKNITLVGGNGDGQTCKVANQIIVALNIEAVSEALVFASKAGADPVRVRQALMGGFASSRILEVHGERMINRTFEPGFKIALHQKDLNLALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSAMVQALELMANHKL 291
               SCOP domains d1yb4a1 A:1-160 automated matches                                                                                                                               d1yb4a2 A:161-291 automated matches                                                                                                 SCOP domains
               CATH domains -1yb4A01 A:2-158 NAD(P)-binding Rossmann-like Domain                                                                                                          1yb4A02 A:159-291 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhh..eeee......hhhhhh.......hhhhhhhh..eeee...hhhhhhhhhhh...........eeeee....hhhhhhhhhhhhhh..eeeee..eehhhhhhhhh.eeeeee.hhhhhhhhhhhhhhheeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yb4 A   1 mKLGFIGLGImGSPmAINLARAGHQLHVTTIGPVADELLSLGAVNVETARQVTEFADIIFImVPDTPQVEDVLFGEHGCAKTSLQGKTIVDmSSISPIETKRFAQRVNEmGADYLDAPVSGGEIGAREGTLSImVGGEQKVFDRVKPLFDILGKNITLVGGNGDGQTCKVANQIIVALNIEAVSEALVFASKAGADPVRVRQALmGGFASSRILEVHGERmINRTFEPGFKIALHQKDLNLALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSAmVQALELmANHKL 291
                            |       10|   |   20        30        40        50        60 |      70        80        90 |     100       110       120       130   |   140       150       160       170       180       190       200    |  210       220|      230       240       250       260       270       280     | 290 
                            |        11-MSE                                             62-MSE                        92-MSE           110-MSE                 134-MSE                                                                205-MSE         221-MSE                                                   279-MSE  |     
                            1-MSE        15-MSE                                                                                                                                                                                                                                                                        286-MSE 


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with Q8ZR83_SALTY | Q8ZR83 from UniProtKB/TrEMBL  Length:292

    Alignment length:291
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
         Q8ZR83_SALTY     1 MKLGFIGLGIMGSPMAINLARAGHQLHVTTIGPVADELLSLGAVNVETARQVTEFADIIFIMVPDTPQVEDVLFGEHGCAKTSLQGKTIVDMSSISPIETKRFAQRVNEMGADYLDAPVSGGEIGAREGTLSIMVGGEQKVFDRVKPLFDILGKNITLVGGNGDGQTCKVANQIIVALNIEAVSEALVFASKAGADPVRVRQALMGGFASSRILEVHGERMINRTFEPGFKIALHQKDLNLALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSAMVQALELMANHKL 291
               SCOP domains d1yb4b1 B:1-160 automated matches                                                                                                                               d1yb4b2 B:161-291 automated matches                                                                                                 SCOP domains
               CATH domains -1yb4B01 B:2-158 NAD(P)-binding Rossmann-like Domain                                                                                                          1yb4B02 B:159-291 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                           CATH domains
           Pfam domains (1) NAD_binding_2-1yb4B01 B:1-162                                                                                                                                     --------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) NAD_binding_2-1yb4B02 B:1-162                                                                                                                                     --------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeee....hhhhhhhhhhh...eeeee.....hhhhhh...ee..hhhhhhhhh.eeee...hhhhhhhhhhh..hhhhh.....eeee....hhhhhhhhhhhhhh...eeee..eehhhhhhhh..eeeeee.hhhhhhhhhhhhhhheeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yb4 B   1 mKLGFIGLGImGSPmAINLARAGHQLHVTTIGPVADELLSLGAVNVETARQVTEFADIIFImVPDTPQVEDVLFGEHGCAKTSLQGKTIVDmSSISPIETKRFAQRVNEmGADYLDAPVSGGEIGAREGTLSImVGGEQKVFDRVKPLFDILGKNITLVGGNGDGQTCKVANQIIVALNIEAVSEALVFASKAGADPVRVRQALmGGFASSRILEVHGERmINRTFEPGFKIALHQKDLNLALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSAmVQALELmANHKL 291
                            |       10|   |   20        30        40        50        60 |      70        80        90 |     100       110       120       130   |   140       150       160       170       180       190       200    |  210       220|      230       240       250       260       270       280     | 290 
                            1-MSE    11-MSE                                             62-MSE                        92-MSE           110-MSE                 134-MSE                                                                205-MSE         221-MSE                                                   279-MSE  |     
                                         15-MSE                                                                                                                                                                                                                                                                        286-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, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8ZR83_SALTY | Q8ZR83)
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: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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