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(-) Description

Title :  RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH CDP
 
Authors :  M. D. Hartmann, M. Ammelburg, S. Djuranovic, J. Martin, A. N. Lupas, K. Zeth
Date :  16 Sep 07  (Deposition) - 20 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Cradle-Loop Barrel, Ctp-Dependent Kinase, Fmn (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ammelburg, M. D. Hartmann, S. Djuranovic, V. Alva, K. K. Koretke, J. Martin, G. Sauer, V. Truffault, K. Zeth, A. N. Lupas, M. Coles
A Ctp-Dependent Archaeal Riboflavin Kinase Forms A Bridge In The Evolution Of Cradle-Loop Barrels.
Structure V. 15 1577 2007
PubMed-ID: 18073108  |  Reference-DOI: 10.1016/J.STR.2007.09.027

(-) Compounds

Molecule 1 - RIBOFLAVIN KINASE
    Chains: A
    EC Number: 2.7.1.161
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: METHANOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: UNCHARACTERIZED PROTEIN MJ0056

 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
1CDP1Ligand/IonCYTIDINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3MRD3Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , LEU A:15 , GLY A:16 , GLU A:17 , GLY A:18 , ARG A:19 , TYR A:40 , GLY A:42 , THR A:43 , LEU A:44 , ASN A:45 , MET A:112 , LYS A:113 , LEU A:114 , ARG A:115 , MG A:1134 , HOH A:2058 , HOH A:2145 , HOH A:2146 , HOH A:2147 , HOH A:2148 , HOH A:2149 , HOH A:2150BINDING SITE FOR RESIDUE CDP A1133
2AC2SOFTWARETHR A:43 , ASN A:45 , CDP A:1133 , HOH A:2146BINDING SITE FOR RESIDUE MG A1134
3AC3SOFTWAREGLU A:17 , TYR A:20BINDING SITE FOR RESIDUE MRD A1135
4AC4SOFTWARELEU A:22 , TYR A:27 , VAL A:94 , PRO A:96 , GLU A:107 , HOH A:2151 , HOH A:2152BINDING SITE FOR RESIDUE MRD A1136
5AC5SOFTWARELEU A:4 , ILE A:80 , LEU A:129 , LYS A:131 , HOH A:2098BINDING SITE FOR RESIDUE MRD A1137

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VBU)

(-) 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:131
 aligned with RIFK_METJA | Q60365 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:131
                               1                                                                                                                               
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127 
           RIFK_METJA     - ---MIIEGEVVSGLGEGRYFLSLPPYKEIFKKILGFEPYEGTLNLKLDREFDINKFKYIETEDFEFNGKRFFGVKVLPIKILIGNKKIDGAIVVPKKTYHSSEIIEIIAPMKLREQFNLKDGDVIKILIKG 128
               SCOP domains d2vbua_ A: CTP-dependent riboflavin kinase, Rfk                                                                                     SCOP domains
               CATH domains -2vbuA01 A:3-132 Riboflavin kinase-like                                                                                             CATH domains
               Pfam domains ---------CTP-dep_RFKase-2vbuA01 A:11-130                                                                                         -- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeehhhhh..ee...eee..eee..eeeeeeeeee..eeeeeeeeee......eeeeeee...hhhhhh......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vbu A   2 VKLMIIEGEVVSGLGEGRYFLSLPPYKEIFKKILGFEPYEGTLNLKLDREFDINKFKYIETEDFEFNGKRFFGVKVLPIKILIGNKKIDGAIVVPKKTYHSSEIIEIIAPMKLREQFNLKDGDVIKILIKG 132
                                    11        21        31        41        51        61        71        81        91       101       111       121       131
   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: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CTP-dep_RFKase] (5)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RIFK_METJA | Q60365)
molecular function
    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: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:0008531    riboflavin kinase activity    Catalysis of the reaction: ATP + riboflavin = ADP + FMN + 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:0009398    FMN biosynthetic process    The chemical reactions and pathways resulting in the formation of FMN, the oxidized form of flavin mononucleotide (riboflavin 5'-(dihydrogen phosphate)), which acts as a coenzyme for a number of oxidative enzymes including NADH dehydrogenase.
    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:0009231    riboflavin biosynthetic process    The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).

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  2.7.1.161
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 Related Entries

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

UniProtKB/Swiss-Prot
        RIFK_METJA | Q60365: 2oyn 2p3m 2vbs 2vbt 2vbv

(-) Related Entries Specified in the PDB File

2p3m SOLUTION STRUCTURE OF MJ0056
2vbs RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH PO4
2vbt RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH CDP AND PO4
2vbv RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH CDP AND FMN