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(-) Description

Title :  CRYSTAL STRUCTURE OF SHIKIMATE KINASE
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Transferase (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 KINASE
    Chains: A, B
    EC Number: 2.7.1.71
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AROK
    Organism Scientific: CAMPYLOBACTER JEJUNI
    Organism Taxid: 197

 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
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMSE B:13 , GLY B:14 , SER B:15 , GLY B:16 , LYS B:17 , SER B:18 , HOH B:188 , HOH B:196 , HOH B:240 , HOH B:323BINDING SITE FOR RESIDUE SO4 B 176
2AC2SOFTWAREARG B:60 , GLY B:82 , GLY B:83 , ARG B:134 , HOH B:183 , HOH B:252 , HOH B:338BINDING SITE FOR RESIDUE SO4 B 177
3AC3SOFTWAREARG A:60 , GLY A:82 , GLY A:83 , LEU A:130 , ARG A:134 , HOH A:183 , HOH A:220BINDING SITE FOR RESIDUE SO4 A 176

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VIA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VIA)

(-) 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:161
 aligned with Q0PBC3_CAMJE | Q0PBC3 from UniProtKB/TrEMBL  Length:165

    Alignment length:161
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164 
         Q0PBC3_CAMJE     5 KNIVFIGFMGSGKSTLARALAKDLDLVFLDSDFLIEQKFNQKVSEIFEQKRENFFREQEQKMADFFSSCEKACIATGGGFVNVSNLEKAGFCIYLKADFEYLKKRLDKDEISKRPLFYDEIKAKKLYNERLSKYEQKANFILNIENKNIDELLSEIKKVIK 165
               SCOP domains d1viaa_ A: Shikimate kinase (AroK)                                                                                                                                SCOP domains
               CATH domains 1viaA00 A:5-165 P-loop containing nucleotide triphosphate hydrolases                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhh.hhhhhheeeeee.hhhhhh...hhhhh.......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1via A   5 KNIVFIGFmGSGKSTLARALAKDLDLVFLDSDFLIEQKFNQKVSEIFEQKRENFFREQEQKmADFFSSCEKACIATGGGFVNVSNLEKAGFCIYLKADFEYLKKRLDKDEISKRPLFYDEIKAKKLYNERLSKYEQKANFILNIENKNIDELLSEIKKVIK 165
                                    14        24        34        44        54        64 |      74        84        94       104       114       124       134       144       154       164 
                                   13-MSE                                               66-MSE                                                                                               


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with Q0PBC3_CAMJE | Q0PBC3 from UniProtKB/TrEMBL  Length:165

    Alignment length:165
                                                                                                                                                                                             165 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   | 
         Q0PBC3_CAMJE     2 MKAKNIVFIGFMGSGKSTLARALAKDLDLVFLDSDFLIEQKFNQKVSEIFEQKRENFFREQEQKMADFFSSCEKACIATGGGFVNVSNLEKAGFCIYLKADFEYLKKRLDKDEISKRPLFYDEIKAKKLYNERLSKYEQKANFILNIENKNIDELLSEIKKVIK-   -
               SCOP domains d1viab_ B: Shikimate kinase (AroK)                                                                                                                                    SCOP domains
               CATH domains 1viaB00 B:2-166 P-loop containing nucleotide triphosphate hydrolases                                                                                                  CATH domains
           Pfam domains (1) -----------SKI-1viaB01 B:13-165                                                                                                                                     - Pfam domains (1)
           Pfam domains (2) -----------SKI-1viaB02 B:13-165                                                                                                                                     - Pfam domains (2)
         Sec.struct. author .....eeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhh.hhhhhheeeeee.hhhhhh...-----------.hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1via B   2 SLAKNIVFIGFmGSGKSTLARALAKDLDLVFLDSDFLIEQKFNQKVSEIFEQKRENFFREQEQKmADFFSSCEKACIATGGGFVNVSNLEKAGFCIYLKADFEYLKKRL-----------YDEIKAKKLYNERLSKYEQKANFILNIENKNIDELLSEIKKVIKE 166
                                    11 |      21        31        41        51        61    |   71        81        91       101        |-         -|      131       141       151       161     
                                      13-MSE                                               66-MSE                                     110         122
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: SKI (16)
(-)
Campylobacter jejuni (1)
1aSKI-1viaB01B:13-165
1bSKI-1viaB02B:13-165

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q0PBC3_CAMJE | Q0PBC3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004765    shikimate kinase activity    Catalysis of the reaction: ATP + shikimate = 3-phosphoshikimate + ADP + 2 H(+).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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