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(-) Description

Title :  SHIKIMATE KINASE FROM HELICOBACTER PYLORI IN COMPLEX WITH SHIKIMATE-3-PHOSPHATE AND ADP
 
Authors :  W. C. Cheng, T. J. Chen, S. C. Lin, W. C. Wang
Date :  03 May 10  (Deposition) - 04 May 11  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Helix-Sheet Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. C. Cheng, Y. F. Chen, H. J. Wang, K. C. Hsu, S. C. Lin, T. J. Chen, J. M. Yang, W. C. Wang
Structures Of Helicobacter Pylori Shikimate Kinase Reveal A Selective Inhibitor-Induced-Fit Mechanism
Plos One V. 7 33481 2012
PubMed-ID: 22438938  |  Reference-DOI: 10.1371/JOURNAL.PONE.0033481

(-) Compounds

Molecule 1 - SHIKIMATE KINASE
    Chains: A
    EC Number: 2.7.1.71
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: JM109
    Expression System Taxid: 85962
    Expression System Vector Type: PLASMID
    Gene: AROK
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Strain: 26695
    Synonym: SK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2S3P1Ligand/IonSHIKIMATE-3-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , SER A:12 , GLY A:13 , LYS A:14 , SER A:15 , SER A:16 , MET A:99 , ARG A:107 , ARG A:116 , ALA A:146 , GLY A:148 , GLY A:149 , LEU A:150 , S3P A:201BINDING SITE FOR RESIDUE ADP A 202
2AC2SOFTWAREMET A:10 , LYS A:14 , ASP A:33 , VAL A:44 , ARG A:57 , GLY A:79 , GLY A:80 , GLY A:81 , ARG A:116 , PRO A:117 , LEU A:118 , ARG A:132 , HOH A:166 , HOH A:171 , HOH A:172 , ADP A:202 , HOH A:220BINDING SITE FOR RESIDUE S3P A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MUF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MUF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MUF)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIKIMATE_KINASEPS01128 Shikimate kinase signature.AROK_HELPY57-83  1A:57-83

(-) Exons   (0, 0)

(no "Exon" information available for 3MUF)

(-) 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:160
 aligned with AROK_HELPY | P56073 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
           AROK_HELPY     2 QHLVLIGFMGSGKSSLAQELGLALKLEVLDTDMIISERVGLSVREIFEELGEDNFRMFEKNLIDELKTLKTPHVISTGGGIVMHENLKGLGTTFYLKMDFETLIKRLNQKEREKRPLLNNLTQAKELFEKRQALYEKNASFIIDARGGLNNSLKQVLQFI 161
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------SKI-3mufA01 A:10-161                                                                                                                                     Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhh...eeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh......eee...hhhhhhhhh..eeeeeee.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------SHIKIMATE_KINASE           ------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3muf A   2 QHLVLIGFMGSGKSSLAQELGLALKLEVLDTDMIISERVGLSVREIFEELGEDNFRMFEKNLIDELKTLKTPHVISTGGGIVMHENLKGLGTTFYLKMDFETLIKRLNQKEREKRPLLNNLTQAKELFEKRQALYEKNASFIIDARGGLNNSLKQVLQFI 161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
   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 3MUF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MUF)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AROK_HELPY | P56073)
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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  AROK_HELPY | P56073
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  2.7.1.71
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 Related Entries

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

UniProtKB/Swiss-Prot
        AROK_HELPY | P56073: 1zuh 1zui 3hr7 3mrs 3n2e

(-) Related Entries Specified in the PDB File

1zuh THE SAME PROTEIN
1zui THE SAME PROTEIN COMPLEXED WITH SHIKIMATE
3hr7 DIMERIC TYPE
3mrs SITE-DIRECTED MUTAGENESIS OF R57 RESIDUE