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(-) Description

Title :  CRYSTAL STRUCTURE OF SHIKIMATE-5-DEHYDROGENASE WITH NAD
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SHIKIMATE 5-DEHYDROGENASE 2
    Chains: A, B
    EC Number: 1.1.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YDIB, B1692, C2087
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric/Biological Unit (3, 24)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:67 , MSE A:68 , PRO A:69 , ASN A:70 , LYS A:71 , GLN A:72BINDING SITE FOR RESIDUE SO4 A 299
2AC2SOFTWAREMSE B:68 , PRO B:69 , ASN B:70 , LYS B:71 , GLN B:72 , HOH B:316 , HOH B:356BINDING SITE FOR RESIDUE SO4 B 299
3AC3SOFTWAREGLY 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 , MSE A:208 , CYS A:232 , VAL A:233 , TYR A:234 , GLY A:255 , MSE A:258 , LEU A:259 , HOH A:313 , HOH A:327 , HOH A:328 , HOH A:329 , HOH A:334 , HOH A:398 , HOH A:399 , HOH A:402BINDING SITE FOR RESIDUE NAD A 300
4AC4SOFTWAREASP B:107 , 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 , MSE B:208 , CYS B:232 , VAL B:233 , TYR B:234 , GLY B:255 , MSE B:258 , LEU B:259 , HOH B:304 , HOH B:309 , HOH B:315 , HOH B:335 , HOH B:351 , HOH B:394 , HOH B:400 , HOH B:409 , HOH B:425BINDING SITE FOR RESIDUE NAD B 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VI2)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Tyr A:15 -Pro A:16
2Mse A:68 -Pro A:69
3Lys A:209 -Pro A:210
4Asn A:235 -Pro A:236
5Tyr B:15 -Pro B:16
6Mse 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 1VI2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VI2)

(-) Exons   (0, 0)

(no "Exon" information available for 1VI2)

(-) 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:284
 aligned with YDIB_ECOLI | P0A6D5 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:284
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    
           YDIB_ECOLI     5 AKYELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALKMRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMGFGA 288
               SCOP domains d1vi2a2 A:5-106 Putative shikimate dehydrogenase YdiB                                                 d1vi2a1 A:107-288 Putative shikimate dehydrogenase YdiB                                                                                                                                SCOP domains
               CATH domains 1vi2A01 A:5-107,A:259-288 Leucine Dehydrogenase, chain A, domain 1                                     1vi2A02 A:108-257 NAD(P)-binding Rossmann-like Domain                                                                                                 -1vi2A01 A:5-107,A:259-288      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh...eeee.....hhhhhhh.eehhhhhhhh...eeeee..eeeeehhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh..eeee................hhhhh....eeee.......hhhhhhhhh...eeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vi2 A   5 AKYELIGLmAYPIRHSLSPEmQNKALEKAGLPFTYmAFEVDNDSFPGAIEGLKALKmRGTGVSmPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDIKGKTmVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGmKPLENESLVNDISLLHPGLLVTECVYNPHmTKLLQQAQQAGCKTIDGYGmLLWQGAEQFTLWTGKDFPLEYVKQVmGFGA 288
                                    14        24|       34     |  44        54      | 64   |    74        84        94       104       114       124  |    134       144       154       164       174       184       194       204   |   214       224       234   |   244       254   |   264       274       284    
                                   13-MSE      25-MSE         40-MSE               61-MSE 68-MSE                                                    127-MSE                                                                          208-MSE                       238-MSE             258-MSE                   284-MSE


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with YDIB_ECOLI | P0A6D5 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:282
                                    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_ECOLI     6 KYELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALKMRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMGFG 287
               SCOP domains d1vi2b2 B:6-106 Putative shikimate dehydrogenase YdiB                                                d1vi2b1 B:107-287 Putative shikimate dehydrogenase YdiB                                                                                                                               SCOP domains
               CATH domains 1vi2B01 B:6-107,B:259-287 Leucine Dehydrogenase, chain A, domain 1                                    1vi2B02 B:108-257 NAD(P)-binding Rossmann-like Domain                                                                                                 -1vi2B01 B:6-107,B:259-287     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhh..eeee...hhhhhhhhh.eehhhhhhhh...eeeee..eeeeehhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh..eeee................hhhhh....eeee.......hhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vi2 B   6 KYELIGLmAYPIRHSLSPEmQNKALEKAGLPFTYmAFEVDNDSFPGAIEGLKALKmRGTGVSmPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDIKGKTmVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGmKPLENESLVNDISLLHPGLLVTECVYNPHmTKLLQQAQQAGCKTIDGYGmLLWQGAEQFTLWTGKDFPLEYVKQVmGFG 287
                                   |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  
                                  13-MSE      25-MSE         40-MSE               61-MSE 68-MSE                                                    127-MSE                                                                          208-MSE                       238-MSE             258-MSE                   284-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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VI2)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YDIB_ECOLI | P0A6D5)
molecular function
    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: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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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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  1vi2
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 Related Entries

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

UniProtKB/Swiss-Prot
        YDIB_ECOLI | P0A6D5: 1npd 1o9b

(-) Related Entries Specified in the PDB File

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