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(-) Description

Title :  STREPTOCOCCUS PNEUMONIAE MEVALONATE KINASE IN COMPLEX WITH DIPHOSPHOMEVALONATE
 
Authors :  J. L. Andreassi, P. W. Bilder, M. W. Vetting, S. L. Roderick, T. S. Leyh
Date :  10 Jan 07  (Deposition) - 01 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Enzyme-Inhibitor Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Andreassi, P. W. Bilder, M. W. Vetting, S. L. Roderick, T. S. Leyh
Crystal Structure Of The Streptococcus Pneumoniae Mevalonate Kinase In Complex With Diphosphomevalonate.
Protein Sci. V. 16 983 2007
PubMed-ID: 17400916  |  Reference-DOI: 10.1110/PS.072755707
(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 BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MVK
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1DP61Ligand/Ion(3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1DP62Ligand/Ion(3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:92 , ASP A:135 , DP6 A:300 , HOH A:458BINDING SITE FOR RESIDUE MG A 400
2AC2SOFTWARELYS A:13 , HIS A:20 , VAL A:22 , VAL A:23 , SER A:91 , SER A:92 , PRO A:131 , SER A:132 , ASP A:135 , THR A:175 , GLY A:255 , GLY A:256 , MG A:400 , HOH A:409 , HOH A:448BINDING SITE FOR RESIDUE DP6 A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OI2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OI2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OI2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OI2)

(-) Exons   (0, 0)

(no "Exon" information available for 2OI2)

(-) Sequences/Alignments

Asymmetric 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:285
 aligned with A0A0H2UNK6_S | A0A0H2UNK6 from UniProtKB/TrEMBL  Length:292

    Alignment length:289
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283         
         A0A0H2UNK6_S     4 KVGVGQAHSKIILIGEHAVVYGYPAISLPLLEVEVTCKVVPAESPWRLYEEDTLSMAVYASLEYLNITEACIRCEIDSAIPEKRGMGSSAAISIAAIRAVFDYYQADLPHDVLEILVNRAEMIAHMNPSGLDAKTCLSDQPIRFIKNVGFTELEMDLSAYLVIADTGVYGHTREAIQVVQNKGKDALPFLHALGELTQQAEVAISQKDAEGLGQILSQAHLHLKEIGVSSPEADFLVETTLSHGALGAKMSGGGLGGCIIALVTNLTHAQELAERLEEKGAVQTWIESL 292
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------GHMP_    kinases_N-2oi2A01 A:76-143                                 ------------------------------------------------------GHMP_kinases_C-2oi2A02 A:198-285                                                        ------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..hhhhhh..eeeeeeeeeeeeeeeee..........hhhhhhhhhhhhhhh.....eeeee.----.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhh....eeee...eeee.......eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....eeeee......eeeeee.hhhhhhhhhhhhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oi2 A   4 KVGVGQAHSKIILIGEHAVVYGYPAISLPLLEVEVTCKVVPAESPWRLYEEDTLSMAVYASLEYLNITEACIRCEID----EKRGMGSSAAISIAAIRAVFDYYQADLPHDVLEILVNRAEMIAHMNPSGLDAKTCLSDQPIRFIKNVGFTELEMDLSAYLVIADTGVYGHTREAIQVVQNKGKDALPFLHALGELTQQAEIAISQKDAEGLGQILSQAHLHLKEIGVSSLEADSLVETALSHGALGAKMSGGGLGGCIIALVTNLTHAQELAERLEEKGAVQTWIESL 292
                                    13        23        33        43        53        63        73      |  - |      93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283         
                                                                                                       80   85                                                                                                                                                                                                               


Chain A from PDB  Type:PROTEIN  Length:285
 aligned with Q8DR51_STRR6 | Q8DR51 from UniProtKB/TrEMBL  Length:292

    Alignment length:289
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283         
         Q8DR51_STRR6     4 KVGVGQAHSKIILIGEHAVVYGYPAISLPLLEVEVTCKVVPAESPWRLYEEDTLSMAVYASLEYLNITEACIRCEIDSAIPEKRGMGSSAAISIAAIRAVFDYYQADLPHDVLEILVNRAEMIAHMNPSGLDAKTCLSDQPIRFIKNVGFTELEMDLSAYLVIADTGVYGHTREAIQVVQNKGKDALPFLHALGELTQQAEIAISQKDAEGLGQILSQAHLHLKEIGVSSLEADSLVETALSHGALGAKMSGGGLGGCIIALVTNLTHAQELAERLEEKGAVQTWIESL 292
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------GHMP_    kinases_N-2oi2A01 A:76-143                                 ------------------------------------------------------GHMP_kinases_C-2oi2A02 A:198-285                                                        ------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..hhhhhh..eeeeeeeeeeeeeeeee..........hhhhhhhhhhhhhhh.....eeeee.----.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhh....eeee...eeee.......eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....eeeee......eeeeee.hhhhhhhhhhhhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oi2 A   4 KVGVGQAHSKIILIGEHAVVYGYPAISLPLLEVEVTCKVVPAESPWRLYEEDTLSMAVYASLEYLNITEACIRCEID----EKRGMGSSAAISIAAIRAVFDYYQADLPHDVLEILVNRAEMIAHMNPSGLDAKTCLSDQPIRFIKNVGFTELEMDLSAYLVIADTGVYGHTREAIQVVQNKGKDALPFLHALGELTQQAEIAISQKDAEGLGQILSQAHLHLKEIGVSSLEADSLVETALSHGALGAKMSGGGLGGCIIALVTNLTHAQELAERLEEKGAVQTWIESL 292
                                    13        23        33        43        53        63        73      |  - |      93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283         
                                                                                                       80   85
   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 2OI2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OI2)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: S5 (103)
(-)
Clan: no clan defined [family: GHMP_kinases_C] (13)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8DR51_STRR6 | Q8DR51)
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: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: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: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.

Chain A   (A0A0H2UNK6_S | A0A0H2UNK6)

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