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(-) Description

Title :  CRYSTAL STRUCTURE OF MEVALONATE KINASE
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym./Biol. Unit :  A
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 - MEVALONATE KINASE
    Chains: A
    EC Number: 2.7.1.36
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MVK, MJ1087
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: MK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1DIO1Ligand/Ion1,4-DIETHYLENE DIOXIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:106 , GLY A:110 , SER A:111 , SER A:112 , HOH A:363BINDING SITE FOR RESIDUE DIO A 323

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GHMP_KINASES_ATPPS00627 GHMP kinases putative ATP-binding domain.MVK_METJA103-114  1A:103-114

(-) Exons   (0, 0)

(no "Exon" information available for 1VIS)

(-) 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:314
 aligned with MVK_METJA | Q58487 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:314
                             1                                                                                                                                                                                                                                                                                                                    312 
                             |       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       279       289       299       309  | 
            MVK_METJA     - -MIIETPSKVILFGEHAVVYGYRAISMAIDLTSTIEIKETQEDEIILNLNDLNKSLGLNLNEIKNINPNNFGDFKYCLCAIKNTLDYLNIEPKTGFKINISSKIPISCGLGSSASITIGTIKAVSGFYNKELKDDEIAKLGYMVEKEIQGKASITDTSTITYKGILEIKNNKFRKIKGEFEEFLKNCKFLIVYAEKRKKKTAELVNEVAKIENKDEIFKEIDKVIDEALKIKNKEDFGKLMTKNHELLKKLNISTPKLDRIVDIGNRFGFGAKLTGAGGGGCVIILVNEEKEKELLKELNKEDVRIFNCRMMN-   -
               SCOP domains d1visa1 A:0-180 Mevalonate kinase                                                                                                                                                    d1visa2 A:181-313 Mevalonate kinase                                                                                                   SCOP domains
               CATH domains -1visA01 A:1-176  [code=3.30.230.10, no name defined]                                                                                                                            1visA02 A:177-307  [code=3.30.70.890, no name defined]                                                                             ------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee..hhhhhh.eeeeeeeeeeeeeeeee....eeeeee....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhh.eeeee..eeee.hhhhhhhhhh..eeeeeee....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.eeeee.....eeeeee....hhhhhhhhhhh...eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------GHMP_KINASES------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vis A   0 SLIIETPSKVILFGEHAVVYGYRAISMAIDLTSTIEIKETQEDEIILNLNDLNKSLGLNLNEIKNINPNNFGDFKYCLCAIKNTLDYLNIEPKTGFKINISSKIPISCGLGSSASITIGTIKAVSGFYNKELKDDEIAKLGYMVEKEIQGKASITDTSTITYKGILEIKNNKFRKIKGEFEEFLKNCKFLIVYAEKRKKKTAELVNEVAKIENKDEIFKEIDKVIDEALKIKNKEDFGKLMTKNHELLKKLNISTPKLDRIVDIGNRFGFGAKLTGAGGGGCVIILVNEEKEKELLKELNKEDVRIFNCRMMNE 313
                                     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       279       289       299       309
   Legend:   → Mismatch (orange background)
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  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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MVK_METJA | Q58487)
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:0004496    mevalonate kinase activity    Catalysis of the reaction: (R)-mevalonate + ATP = (R)-5-phosphomevalonate + ADP + 2 H(+).
    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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    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:0019287    isopentenyl diphosphate biosynthetic process, mevalonate pathway    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate, via the intermediate mevalonate. This pathway converts acetate, in the form of acetyl-CoA, to isopentenyl diphosphate (IPP), the fundamental unit in isoprenoid biosynthesis, through a series of mevalonate intermediates.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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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 Related Entries

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

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        MVK_METJA | Q58487: 1kkh

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