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(-) Description

Title :  CRYSTAL STRUCTURE OF SHIKIMATE 5-DEHYDROGENASE (AROE) FROM GEOBACILLUS KAUSTOPHILUS
 
Authors :  B. Bagautdinov, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 Feb 07  (Deposition) - 18 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Shikimate, Dimer, X-Ray Diffraction, 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 Structure Of Shikimate 5-Dehydrogenase (Aroe) From Geobacillus Kaustophilus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) 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: GEOBACILLUS KAUSTOPHILUS
    Organism Taxid: 1462
    Synonym: AROE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:265 , GLN A:269BINDING SITE FOR RESIDUE CL A 1001
2AC2SOFTWAREASN A:113 , ARG A:116 , ARG A:180 , HOH A:1075BINDING SITE FOR RESIDUE CL A 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:31 -Pro A:32
2Ile A:84 -Pro A:85
3His A:217 -Pro A:218
4Asn A:242 -Pro A:243
5Phe B:31 -Pro B:32
6Ile B:84 -Pro B:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2EGG)

(-) 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:278
 aligned with AROE_GEOKA | Q5KWX7 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:278
                              1                                                                                                                                                                                                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268        
           AROE_GEOKA     - --MEKVYGLIGFPVEHSLSPLMHNDAFARLGIPARYHLFSVEPGQVGAAIAGVRALGIAGVNVTIPHKLAVIPFLDEVDEHARRIGAVNTIINNDGRLVGYNTDGLGYVQALEEEMNITLDGKRILVIGAGGGARGIYFSLLSTAAERIDMANRTVEKAERLVREGDERRSAYFSLAEAETRLAEYDIIINTTSVGMHPRVEVQPLSLERLRPGVIVSDIIYNPLETKWLKEAKARGARVQNGVGMLVYQGALAFEKWTGQWPDVNRMKQLVIEALRR 276
               SCOP domains d2egga1 A:20-122 Shikimate 5-dehydrogenase AroE                                                        d2egga2 A:123-297 Shikimate 5-dehydrogenase AroE                                                                                                                                SCOP domains
               CATH domains 2eggA01 A:20-121,A:262-297 Leucine Dehydrogenase, chain A, domain 1                                   2eggA02 A:122-261 NAD(P)-binding Rossmann-like Domain                                                                                       2eggA01 A:20-121,A:262-297           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee......hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhh..eeee.......hhhhh.eehhhhhhhh...eeeee..eeeee.hhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh......eehhhhhhhhhhhh.eeee........................eeee.......hhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2egg A  20 GHMEKVYGLIGFPVEHSLSPLMHNDAFARLGIPARYHLFSVEPGQVGAAIAGVRALGIAGVNVTIPHKLAVIPFLDEVDEHARRIGAVNTIINNDGRLVGYNTDGLGYVQALEEEMNITLDGKRILVIGAGGGARGIYFSLLSTAAERIDMANRTVEKAERLVREGDERRSAYFSLAEAETRLAEYDIIINTTSVGMHPRVEVQPLSLERLRPGVIVSDIIYNPLETKWLKEAKARGARVQNGVGMLVYQGALAFEKWTGQWPDVNRMKQLVIEALRR 297
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289        


Chain B from PDB  Type:PROTEIN  Length:166
 aligned with AROE_GEOKA | Q5KWX7 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:276
                             1                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269      
           AROE_GEOKA     - -MEKVYGLIGFPVEHSLSPLMHNDAFARLGIPARYHLFSVEPGQVGAAIAGVRALGIAGVNVTIPHKLAVIPFLDEVDEHARRIGAVNTIINNDGRLVGYNTDGLGYVQALEEEMNITLDGKRILVIGAGGGARGIYFSLLSTAAERIDMANRTVEKAERLVREGDERRSAYFSLAEAETRLAEYDIIINTTSVGMHPRVEVQPLSLERLRPGVIVSDIIYNPLETKWLKEAKARGARVQNGVGMLVYQGALAFEKWTGQWPDVNRMKQLVIEALR 275
               SCOP domains d2eggb1 B:21-122 Shikimate 5-dehydrogenase AroE                                                       d2eggb2 B:123-296 Shi                                                                                             kimate                  5-dehydrogenase AroE                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhh..eeee.......hhhhh.eehhhhhhhh...eeeee..eeeee.hhhhhhhhhhhhhh........---------------------------------------------------------------------------------------------......-----------------..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2egg B  21 HMEKVYGLIGFPVEHSLSPLMHNDAFARLGIPARYHLFSVEPGQVGAAIAGVRALGIAGVNVTIPHKLAVIPFLDEVDEHARRIGAVNTIINNDGRLVGYNTDGLGYVQALEEEMNITLDGKR---------------------------------------------------------------------------------------------SDIIYN-----------------QNGVGMLVYQGALAFEKWTGQWPDVNRMKQLVIEALR 296
                                    30        40        50        60        70        80        90       100       110       120       130       140  |      -         -         -         -         -         -         -         -         -      |240 |       -       260       270       280       290      
                                                                                                                                                    143                                                                                           237  242               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  (2, 4)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (AROE_GEOKA | Q5KWX7)
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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