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(-) Description

Title :  1.95 ANGSTROM CRYSTAL STRUCTURE OF SHIKIMATE 5-DEHYDROGENASE (AROE) FROM SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM IN COMPLEX WITH NAD
 
Authors :  G. Minasov, S. H. Light, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Win L. Papazisi, W. F. Anderson, Center For Structural Genomics Of I Diseases (Csgid)
Date :  25 Jul 11  (Deposition) - 17 Aug 11  (Release) - 17 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Nad(P)-Binding Rossmann-Fold C-Terminal Domain, Aminoacid Dehydrogenase-Like N-Terminal Domain, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, S. H. Light, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 95 Angstrom Crystal Structure Of Shikimate 5-Dehydrogenas (Aroe) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium In Complex With Nad.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - QUINATE/SHIKIMATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.282
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: AROE, STM1359, YDIB
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371
    Strain: LT2
    Synonym: NAD-DEPENDENT SHIKIMATE 5-DEHYDROGENASE 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:131 , ALA A:132 , GLY A:133 , GLY A:134 , ALA A:135 , ASN A:155 , ARG A:156 , ASP A:158 , PHE A:160 , GLY A:203 , THR A:204 , LYS A:205 , VAL A:206 , MET A:208 , LEU A:211 , CYS A:232 , VAL A:233 , TYR A:234 , GLY A:255 , MET A:258 , LEU A:259 , PO4 A:290 , HOH A:301 , HOH A:304 , HOH A:313 , HOH A:327 , HOH A:456 , HOH A:492 , HOH A:496 , HOH A:510 , HOH A:512 , HOH A:602BINDING SITE FOR RESIDUE NAD A 289
2AC2SOFTWARESER A:67 , LYS A:71 , ASN A:92 , ASP A:107 , NAD A:289 , HOH A:346 , HOH A:375 , HOH A:421 , HOH A:429 , HOH A:492BINDING SITE FOR RESIDUE PO4 A 290
3AC3SOFTWAREGLY B:131 , ALA B:132 , GLY B:133 , GLY B:134 , ALA B:135 , ASN B:155 , ARG B:156 , ASP B:158 , PHE B:160 , GLY B:203 , THR B:204 , LYS B:205 , VAL B:206 , MET B:208 , LEU B:211 , CYS B:232 , TYR B:234 , GLY B:255 , MET B:258 , LEU B:259 , PO4 B:290 , HOH B:293 , HOH B:315 , HOH B:333 , HOH B:355 , HOH B:428 , HOH B:448 , HOH B:452 , HOH B:453 , HOH B:536BINDING SITE FOR RESIDUE NAD B 289
4AC4SOFTWARESER B:67 , LYS B:71 , ASN B:92 , ASP B:107 , NAD B:289 , HOH B:325 , HOH B:351 , HOH B:472BINDING SITE FOR RESIDUE PO4 B 290

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T4E)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Tyr A:15 -Pro A:16
2Met A:68 -Pro A:69
3Lys A:209 -Pro A:210
4Asn A:235 -Pro A:236
5Tyr B:15 -Pro B:16
6Met B:68 -Pro B:69
7Lys B:209 -Pro B:210
8Asn B:235 -Pro B:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T4E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T4E)

(-) Exons   (0, 0)

(no "Exon" information available for 3T4E)

(-) 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:283
 aligned with YDIB_SALTY | Q8ZPR4 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:283
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   
           YDIB_SALTY     6 KYELIGLMAYPIRHSLSPEMQNKALEKAGLPYTYMAFEVDNTTFASAIEGLKALKMRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDMRGKTMVLLGAGGAATAIGAQAAIEGIKEIKLFNRKDDFFEKAVAFAKRVNENTDCVVTVTDLADQHAFTEALASADILTNGTKVGMKPLENESLIGDVSLLRPELLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFELWTGKAFPLDYVKQVMGFTA 288
               SCOP domains d3t4ea1 A:6-106 automated matches                                                                    d3t4ea2 A:107-288 automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhh...eeee...hhhhhhhhh.eehhhhhhhh...eeeee..eeeeehhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhh.eeee................hhhhh....eeee.......hhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhh...hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t4e A   6 KYELIGLMAYPIRHSLSPEMQNKALEKAGLPYTYMAFEVDNTTFASAIEGLKALKMRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDMRGKTMVLLGAGGAATAIGAQAAIEGIKEIKLFNRKDDFFEKAVAFAKRVNENTDCVVTVTDLADQHAFTEALASADILTNGTKVGMKPLENESLIGDVSLLRPELLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFELWTGKAFPLDYVKQVMGFTA 288
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   


Chain B from PDB  Type:PROTEIN  Length:283
 aligned with YDIB_SALTY | Q8ZPR4 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:283
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
           YDIB_SALTY     4 TAKYELIGLMAYPIRHSLSPEMQNKALEKAGLPYTYMAFEVDNTTFASAIEGLKALKMRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDMRGKTMVLLGAGGAATAIGAQAAIEGIKEIKLFNRKDDFFEKAVAFAKRVNENTDCVVTVTDLADQHAFTEALASADILTNGTKVGMKPLENESLIGDVSLLRPELLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFELWTGKAFPLDYVKQVMGF 286
               SCOP domains d3t4eb1 B:4-106 automated matches                                                                      d3t4eb2 B:107-286 automated matches                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee......hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhh...eeee.....hhhhhhh.eehhhhhhhh...eeeee..eeeeehhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhh.eeee................hhhhh....eeee.......hhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t4e B   4 TAKYELIGLMAYPIRHSLSPEMQNKALEKAGLPYTYMAFEVDNTTFASAIEGLKALKMRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDMRGKTMVLLGAGGAATAIGAQAAIEGIKEIKLFNRKDDFFEKAVAFAKRVNENTDCVVTVTDLADQHAFTEALASADILTNGTKVGMKPLENESLIGDVSLLRPELLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFELWTGKAFPLDYVKQVMGF 286
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T4E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T4E)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YDIB_SALTY | Q8ZPR4)
molecular function
    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:0030266    quinate 3-dehydrogenase (NAD+) activity    Catalysis of the reaction: (-)-quinate + NAD+ = (-)-3-dehydroquinate + NADH + H+.
    GO:0052733    quinate 3-dehydrogenase (NADP+) activity    Catalysis of the reaction: quinate + NADP+ = 3-dehydroquinate + NADPH + H+.
    GO:0052734    shikimate 3-dehydrogenase (NAD+) activity    Catalysis of the reaction: shikimate + NAD+ = 3-dehydroshikimate + NADH + H+.
    GO:0004764    shikimate 3-dehydrogenase (NADP+) activity    Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009423    chorismate biosynthetic process    The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
    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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 Related Entries

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