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(-) Description

Title :  CRYSTAL STRUCTURE OF SHIKIMATE 5-DEHYDROGENASE (AROE) FROM THERMUS THERMOPHILUS HB8
 
Authors :  B. Bagautdinov, N. Kunishima, Riken Structural Genomics/Proteomi Initiative (Rsgi)
Date :  21 Jan 05  (Deposition) - 01 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Shikimate, Dimer, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bagautdinov, N. Kunishima
Crystal Structures Of Shikimate Dehydrogenase Aroe From Thermus Thermophilus Hb8 And Its Cofactor And Substrate Complexes: Insights Into The Enzymatic Mechanism
J. Mol. Biol. V. 373 424 2007
PubMed-ID: 17825835  |  Reference-DOI: 10.1016/J.JMB.2007.08.017

(-) Compounds

Molecule 1 - SHIKIMATE 5-DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AROE
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: AROE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:61 , PRO A:62 , LEU A:63 , LYS A:64 , GLU A:65 , HOH A:1653BINDING SITE FOR RESIDUE ACT A 1301
2AC2SOFTWAREARG B:80BINDING SITE FOR RESIDUE ACT B 1302
3AC3SOFTWAREASN B:146 , ARG B:147 , THR B:148 , ARG B:151BINDING SITE FOR RESIDUE ACT B 1303
4AC4SOFTWAREHIS B:70 , HOH B:1405 , HOH B:1504BINDING SITE FOR RESIDUE ACT B 1304
5AC5SOFTWAREGLY B:125 , GLY B:126 , ARG B:151 , ARG B:180 , HOH B:1449 , HOH B:1481 , HOH B:1542BINDING SITE FOR RESIDUE SO4 B 1401
6AC6SOFTWAREPRO A:192 , ARG A:213 , HOH A:1411 , HOH A:1440 , HOH A:1443 , HOH A:1530BINDING SITE FOR RESIDUE SO4 A 1402
7AC7SOFTWAREASN A:146 , THR A:148 , ARG A:151BINDING SITE FOR RESIDUE SO4 A 1403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1His A:9 -Pro A:10
2Leu A:61 -Pro A:62
3Gly A:117 -Pro A:118
4Arg A:208 -Pro A:209
5His B:9 -Pro B:10
6Leu B:61 -Pro B:62
7Gly B:117 -Pro B:118
8Arg B:208 -Pro B:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WXD)

(-) 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:263
 aligned with AROE_THET8 | Q5SJF8 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:263
                                    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   
           AROE_THET8     1 MLRFAVLGHPVAHSLSPAMHAFALESLGLEGSYEAWDTPLEALPGRLKEVRRAFRGVNLTLPLKEAALAHLDWVSPEAQRIGAVNTVLQVEGRLFGFNTDAPGFLEALKAGGIPLKGPALVLGAGGAGRAVAFALREAGLEVWVWNRTPQRALALAEEFGLRAVPLEKAREARLLVNATRVGLEDPSASPLPAELFPEEGAAVDLVYRPLWTRFLREAKAKGLKVQTGLPMLAWQGALAFRLWTGLLPDPSGMEEAARRALGV 263
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1wxdA01 A:1-99,A:236-249 Leucine Dehydrogenase, chain A, domain 1                                  ----------------------------------------------------------------------------------------------------------------------------------------1wxdA01       -------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh.eeee......hhhhhh.eehhhhhhhh...eeeee..eeeee.hhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh.ee.hhhhhhhh.eeee..............hhhhh....eeee.......hhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxd A   1 MLRFAVLGHPVAHSLSPAMHAFALESLGLEGSYEAWDTPLEALPGRLKEVRRAFRGVNLTLPLKEAALAHLDWVSPEAQRIGAVNTVLQVEGRLFGFNTDAPGFLEALKAGGIPLKGPALVLGAGGAGRAVAFALREAGLEVWVWNRTPQRALALAEEFGLRAVPLEKAREARLLVNATRVGLEDPSASPLPAELFPEEGAAVDLVYRPLWTRFLREAKAKGLKVQTGLPMLAWQGALAFRLWTGLLPDPSGMEEAARRALGV 263
                                    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   


Chain B from PDB  Type:PROTEIN  Length:263
 aligned with AROE_THET8 | Q5SJF8 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:263
                                    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   
           AROE_THET8     1 MLRFAVLGHPVAHSLSPAMHAFALESLGLEGSYEAWDTPLEALPGRLKEVRRAFRGVNLTLPLKEAALAHLDWVSPEAQRIGAVNTVLQVEGRLFGFNTDAPGFLEALKAGGIPLKGPALVLGAGGAGRAVAFALREAGLEVWVWNRTPQRALALAEEFGLRAVPLEKAREARLLVNATRVGLEDPSASPLPAELFPEEGAAVDLVYRPLWTRFLREAKAKGLKVQTGLPMLAWQGALAFRLWTGLLPDPSGMEEAARRALGV 263
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1wxdB01 B:1-99,B:236-249 Leucine Dehydrogenase, chain A, domain 1                                  ----------------------------------------------------------------------------------------------------------------------------------------1wxdB01       -------------- CATH domains
           Pfam domains (1) -----Shikimate_dh_N-1wxdB03 B:6-87                                                     ---------------------Shikimate_DH-1wxdB01 B:109-205                                                                   ---------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----Shikimate_dh_N-1wxdB04 B:6-87                                                     ---------------------Shikimate_DH-1wxdB02 B:109-205                                                                   ---------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh.eeee.......hhhhh.eehhhhhhhh...eeeee..eeeee.hhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh..ee.hhhhhhhh.eeee..............hhhhh....eeee.......hhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxd B   1 MLRFAVLGHPVAHSLSPAMHAFALESLGLEGSYEAWDTPLEALPGRLKEVRRAFRGVNLTLPLKEAALAHLDWVSPEAQRIGAVNTVLQVEGRLFGFNTDAPGFLEALKAGGIPLKGPALVLGAGGAGRAVAFALREAGLEVWVWNRTPQRALALAEEFGLRAVPLEKAREARLLVNATRVGLEDPSASPLPAELFPEEGAAVDLVYRPLWTRFLREAKAKGLKVQTGLPMLAWQGALAFRLWTGLLPDPSGMEEAARRALGV 263
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 1WXD)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: Shikimate_dh_N] (15)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AROE_THET8 | Q5SJF8)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    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: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.
    GO:0019632    shikimate metabolic process    The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids.

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  1wxd
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 Related Entries

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

UniProtKB/Swiss-Prot
        AROE_THET8 | Q5SJF8: 2cy0 2d5c 2ev9

(-) Related Entries Specified in the PDB File

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