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(-) Description

Title :  RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH PO4
 
Authors :  M. D. Hartmann, S. Djuranovic, M. Ammelburg, J. Martin, A. N. Lupas, K. Zeth
Date :  16 Sep 07  (Deposition) - 20 Nov 07  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Fmn, Cradle-Loop Barrel, Ctp-Dependent Kinase, Transferase (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
    ChainsA
    EC Number2.7.1.161
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificMETHANOCOCCUS JANNASCHII
    Organism Taxid2190
    SynonymPROTEIN MJ0056

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2PO41Ligand/IonPHOSPHATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , LEU A:15 , ARG A:19 , ASN A:45 , GLU A:63 , THR A:99 , HIS A:101 , GLU A:107 , ZN A:1135BINDING SITE FOR RESIDUE PO4 A1134
2AC2SOFTWAREGLU A:63 , HIS A:101 , PO4 A:1134BINDING SITE FOR RESIDUE ZN A1135
3AC3SOFTWARELYS A:113 , LEU A:114BINDING SITE FOR RESIDUE CL A1136
4AC4SOFTWAREGLY A:14 , LYS A:33 , THR A:43 , ASN A:45BINDING SITE FOR RESIDUE CL A1137

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VBS)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:132
 aligned with RIFK_METJA | Q60365 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:132
                               1                                                                                                                                
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127  
           RIFK_METJA     - ---MIIEGEVVSGLGEGRYFLSLPPYKEIFKKILGFEPYEGTLNLKLDREFDINKFKYIETEDFEFNGKRFFGVKVLPIKILIGNKKIDGAIVVPKKTYHSSEIIEIIAPMKLREQFNLKDGDVIKILIKGD 129
               SCOP domains d2vbsa_ A: CTP-dependent riboflavin kinase, Rfk                                                                                      SCOP domains
               CATH domains -2vbsA01 A:3-132 Riboflavin kinase-like                                                                                            - CATH domains
               Pfam domains ---------CTP-dep_RFKase-2vbsA01 A:11-130                                                                                         --- Pfam domains
         Sec.struct. author ...eeeeeeee......hhhhhhhhhhhhhhhhhh.......eeeee....hhhhh..ee...eee..eee...eeeeeeeee..eeeeeeeee.........eeeee...hhhhhh......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vbs A   2 VKLMIIEGEVVSGLGEGRYFLSLPPYKEIFKKILGFEPYEGTLNLKLDREFDINKFKYIETEDFEFNGKRFFGVKVLPIKILIGNKKIDGAIVVPKKTYHSSEIIEIIAPMKLREQFNLKDGDVIKILIKGD 133
                                    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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        RIFK_METJA | Q603652oyn 2p3m 2vbt 2vbu 2vbv

(-) Related Entries Specified in the PDB File

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