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(-) Description

Title :  CRYSTAL STRUCTURE OF SHIKIMATE 5-DEHYDROGENASE (AROE) FROM THERMUS THERMOPHILUS HB8 IN COMPLEX WITH SHIKIMATE
 
Authors :  B. Bagautdinov, N. Kunishima, Riken Structural Genomics/Proteomi Initiative (Rsgi)
Date :  31 Oct 05  (Deposition) - 01 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Shikimate, Substrate, Dimer, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, 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: PET 11A
    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, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1SKM2Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID
2SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:109 , PRO A:192 , ALA A:193 , ARG A:213 , HOH A:1413 , HOH A:1429 , HOH A:1466 , HOH A:1550 , HOH A:1642 , ARG B:162 , HOH B:1480BINDING SITE FOR RESIDUE SO4 A 1401
2AC2SOFTWAREARG A:241 , LEU A:242 , GLN B:89 , VAL B:90 , GLU B:91 , HOH B:1409 , HOH B:1413 , HOH B:1454BINDING SITE FOR RESIDUE SO4 B 1402
3AC3SOFTWAREGLN A:226 , THR A:227 , ARG A:258 , HOH A:1572 , HOH A:1590 , HOH A:1635BINDING SITE FOR RESIDUE SO4 A 1403
4AC4SOFTWAREGLU A:157 , ARG B:180 , ALA B:188 , SER B:189 , THR B:212 , ARG B:213 , PHE B:214BINDING SITE FOR RESIDUE SO4 B 1404
5AC5SOFTWAREVAL A:6 , SER A:14 , SER A:16 , ASN A:58 , LEU A:59 , THR A:60 , LYS A:64 , ASN A:85 , ASP A:100 , TYR A:207 , GLN A:235BINDING SITE FOR RESIDUE SKM A 301
6AC6SOFTWARESER B:14 , SER B:16 , ASN B:58 , THR B:60 , LYS B:64 , ASN B:85 , ASP B:100 , GLN B:235 , HOH B:1421BINDING SITE FOR RESIDUE SKM B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D5C)

(-) Cis Peptide Bonds  (7, 7)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D5C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D5C)

(-) Exons   (0, 0)

(no "Exon" information available for 2D5C)

(-) 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:261
 aligned with AROE_THET8 | Q5SJF8 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:261
                                    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 MLRFAVLGHPVAHSLSPAMHAFALESLGLEGSYEAWDTPLEALPGRLKEVRRAFRGVNLTLPLKEAALAHLDWVSPEAQRIGAVNTVLQVEGRLFGFNTDAPGFLEALKAGGIPLKGPALVLGAGGAGRAVAFALREAGLEVWVWNRTPQRALALAEEFGLRAVPLEKAREARLLVNATRVGLEDPSASPLPAELFPEEGAAVDLVYRPLWTRFLREAKAKGLKVQTGLPMLAWQGALAFRLWTGLLPDPSGMEEAARRAL 261
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2d5cA01 A:1-99,A:236-249 Leucine Dehydrogenase, chain A, domain 1                                  ----------------------------------------------------------------------------------------------------------------------------------------2d5cA01       ------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh.eeee.....hhhhhhh.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
                 2d5c A   1 MLRFAVLGHPVAHSLSPAMHAFALESLGLEGSYEAWDTPLEALPGRLKEVRRAFRGVNLTLPLKEAALAHLDWVSPEAQRIGAVNTVLQVEGRLFGFNTDAPGFLEALKAGGIPLKGPALVLGAGGAGRAVAFALREAGLEVWVWNRTPQRALALAEEFGLRAVPLEKAREARLLVNATRVGLEDPSASPLPAELFPEEGAAVDLVYRPLWTRFLREAKAKGLKVQTGLPMLAWQGALAFRLWTGLLPDPSGMEEAARRAL 261
                                    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:259
 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 2d5cB01 B:1-99,B:236-249 Leucine Dehydrogenase, chain A, domain 1                                  ----------------------------------------------------------------------------------------------------------------------------------------2d5cB01       -------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh.eeee.......hhhhh.eehhhhhhhh...eeeee..eeeee.hhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh.ee.hhhhhhhh.eeee......----....hhhhh....eeee.......hhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d5c B   1 MLRFAVLGHPVAHSLSPAMHAFALESLGLEGSYEAWDTPLEALPGRLKEVRRAFRGVNLTLPLKEAALAHLDWVSPEAQRIGAVNTVLQVEGRLFGFNTDAPGFLEALKAGGIPLKGPALVLGAGGAGRAVAFALREAGLEVWVWNRTPQRALALAEEFGLRAVPLEKAREARLLVNATRVGL----ASPLPAELFPEEGAAVDLVYRPLWTRFLREAKAKGLKVQTGLPMLAWQGALAFRLWTGLLPDPSGMEEAARRALGV 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   
                                                                                                                                                                                                                183  188
   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 2D5C)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D5C)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        AROE_THET8 | Q5SJF8: 1wxd 2cy0 2ev9

(-) Related Entries Specified in the PDB File

1wxd THE SAME PROTEIN IN APO FORM
2cy0 THE SAME PROTEIN IN COMPLEX WITH NADP
2ev9 THE SAME PROTEIN IN COMPLEX WITH NADP AND SHIKIMATE RELATED ID: TTK003000004.4 RELATED DB: TARGETDB