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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS SHIKIMATE KINASE IN COMPLEX WITH SHIKIMATE AND ADP AT 2.15 ANGSTROM RESOLUTION
 
Authors :  B. Dhaliwal, C. E. Nichols, J. Ren, M. Lockyer, I. Charles, A. R. Hawkins, D. K. Stammers
Date :  05 Aug 04  (Deposition) - 19 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Shikimate Pathway, Shikimate Kinase, X-Ray Crystallography, 2 Phorsphoryl Transfer, Drug Design, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Dhaliwal, C. E. Nichols, J. Ren, M. Lockyer, I. Charles, A. R. Hawkins, D. K. Stammers
Crystallographic Studies Of Shikimate Binding And Induced Conformational Changes In Mycobacterium Tuberculosis Shikimate Kinase.
Febs Lett. V. 574 49 2004
PubMed-ID: 15358538  |  Reference-DOI: 10.1016/J.FEBSLET.2004.08.005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SHIKIMATE KINASE
    Chains: A
    EC Number: 2.7.1.71
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET17B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AROK
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: SK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL3Ligand/IonCHLORIDE ION
3SKM1Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:66 , ARG A:160BINDING SITE FOR RESIDUE CL A 190
2AC2SOFTWAREGLY A:29 , HIS A:72 , GLY A:74BINDING SITE FOR RESIDUE CL A 191
3AC3SOFTWAREARG A:66 , ALA A:90 , ARG A:109 , HOH A:264BINDING SITE FOR RESIDUE CL A 192
4AC4SOFTWARELEU A:10 , GLY A:12 , SER A:13 , GLY A:14 , LYS A:15 , SER A:16 , THR A:17 , ARG A:110 , ARG A:117 , ARG A:153 , ASN A:154 , PRO A:155 , HOH A:194 , HOH A:198 , HOH A:199 , HOH A:209 , HOH A:260 , HOH A:274 , HOH A:291BINDING SITE FOR RESIDUE ADP A 180
5AC5SOFTWAREPRO A:11 , ASP A:34 , ARG A:58 , GLY A:79 , GLY A:80 , GLY A:81 , PRO A:118 , LEU A:119 , ARG A:136 , HOH A:193 , HOH A:194 , HOH A:195 , HOH A:197BINDING SITE FOR RESIDUE SKM A 181

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U8A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U8A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U8A)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIKIMATE_KINASEPS01128 Shikimate kinase signature.AROK_MYCTO58-83  1A:58-83
AROK_MYCTU58-83  1A:58-83

(-) Exons   (0, 0)

(no "Exon" information available for 1U8A)

(-) 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:163
 aligned with AROK_MYCTO | P9WPY2 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     
           AROK_MYCTO     2 APKAVLVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIFATDGEQEFRRIEEDVVRAALADHDGVLSLGGGAVTSPGVRAALAGHTVVYLEISAAEGVRRTGGNTVRPLLAGPDRAEKYRALMAKRAPLYRRVATMRVDTNRRNPGAVVRHILSRL 166
               SCOP domains d1u8aa_ A: Shikimate kinase (AroK)                                                                                                                                    SCOP domains
               CATH domains 1u8aA00 A:2-166 P-loop containing nucleotide triphosphate hydrolases                                                                                                  CATH domains
               Pfam domains ---------SKI-1u8aA01 A:11-166                                                                                                                                         Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhh...eeeee.hhhhhhhhh..--........hhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------SHIKIMATE_KINASE          ----------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u8a A   2 APKAVLVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIFATDGEQEFRRIEEDVVRAALADHDGVLSLGGGAVTSPGVRAALAGHTVVYLEISAAEGVRRTGG--VRPLLAGPDRAEKYRALMAKRAPLYRRVATMRVDTNRRNPGAVVRHILSRL 166
                                    11        21        31        41        51        61        71        81        91       101       111 |  |  121       131       141       151       161     
                                                                                                                                         113  |                                                  
                                                                                                                                            116                                                  


Chain A from PDB  Type:PROTEIN  Length:163
 aligned with AROK_MYCTU | P9WPY3 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     
           AROK_MYCTU     2 APKAVLVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIFATDGEQEFRRIEEDVVRAALADHDGVLSLGGGAVTSPGVRAALAGHTVVYLEISAAEGVRRTGGNTVRPLLAGPDRAEKYRALMAKRAPLYRRVATMRVDTNRRNPGAVVRHILSRL 166
               SCOP domains d1u8aa_ A: Shikimate kinase (AroK)                                                                                                                                    SCOP domains
               CATH domains 1u8aA00 A:2-166 P-loop containing nucleotide triphosphate hydrolases                                                                                                  CATH domains
               Pfam domains ---------SKI-1u8aA01 A:11-166                                                                                                                                         Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhh...eeeee.hhhhhhhhh..--........hhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------SHIKIMATE_KINASE          ----------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u8a A   2 APKAVLVGLPGSGKSTIGRRLAKALGVGLLDTDVAIEQRTGRSIADIFATDGEQEFRRIEEDVVRAALADHDGVLSLGGGAVTSPGVRAALAGHTVVYLEISAAEGVRRTGG--VRPLLAGPDRAEKYRALMAKRAPLYRRVATMRVDTNRRNPGAVVRHILSRL 166
                                    11        21        31        41        51        61        71        81        91       101       111 |  |  121       131       141       151       161     
                                                                                                                                         113  |                                                  
                                                                                                                                            116
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (15, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AROK_MYCTO | P9WPY2)
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.

Chain A   (AROK_MYCTU | P9WPY3)
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:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    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.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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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_MYCTO | P9WPY2: 1l4u 1l4y 1we2 1zyu 2dfn 2dft 2g1j 2g1k 2iyq 2iyr 2iys 2iyt 2iyu 2iyv 2iyw 2iyx 2iyy 2iyz 3baf 4bqs
        AROK_MYCTU | P9WPY3: 1l4u 1l4y 1we2 1zyu 2dfn 2dft 2g1j 2g1k 2iyq 2iyr 2iys 2iyt 2iyu 2iyv 2iyw 2iyx 2iyy 2iyz 3baf 4bqs

(-) Related Entries Specified in the PDB File

1l4u CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MGADP AND PT(II) AT 1.8 ANGSTROM RESOLUTION
1l4y CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MGADP AT 2.0 ANGSTROM RESOLUTION