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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOFLAVIN KINASE FROM THERMOPLASMA ACIDOPHILUM
 
Authors :  J. B. Bonanno, M. Rutter, K. T. Bain, M. Mendoza, R. Romero, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  11 Apr 08  (Deposition) - 29 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Transferase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Fmn, Kinase, Magnesium, Metal-Binding, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bonanno, M. Rutter, K. T. Bain, M. Mendoza, R. Romero, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Riboflavin Kinase From Thermoplasma Acidophilum.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOFLAVIN KINASE
    Atcc: 25905
    Chains: A
    EC Number: 2.7.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: RFK, TA1064
    Organism Scientific: THERMOPLASMA ACIDOPHILUM DSM 1728
    Organism Taxid: 273075
    Strain: DSM 1728 / AMRC-C165 / IFO 15155 / JCM 9062

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:187
 aligned with RIFK_THEAC | Q9HJA6 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:216
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214      
           RIFK_THEAC     5 DQYYRAIKKIKEAAEASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTVTKRGQILNITEKGLDVLYTEFADLSRILAIKNNVVITGTVTSGMGEGRYYVARKQYIIQFQEKLGIIPYLGTLNIKVDQASLPELRKIRGFRGIHIEGFKTEDRTFGSVKAFPAKIQNIPCFVIMPERTVYTDVIEIISDKYLREEINLHDGDRVSVEVYT 220
               SCOP domains d3ctaa1 A:5-89 Ta1064 (RFK), N-terminal domain                                       d3ctaa2 A:90            -220 CTP-depend   ent riboflavin kinase, Rfk                                                                SCOP domains
               CATH domains 3ctaA01 A:5-88 'winged helix' repressor DNA binding domain                          3ctaA02 A:89-            220 Riboflavin    kinase-like                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....eee.hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhhhh.....eeeeeee..------------.hhhhhhhhh.....---.eeee...hhhhhhhhhhh..eee.....--.....eeeeeeee..eeeeeeee.......eeeee..------------.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cta A   5 DQYYRAIKKIKEAAEASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTVTKRGQILNITEKGLDVLYTEFADLSRILAIKNNVVITGTVTS------------QYIIQFQEKLGIIPY---LNIKVDQASLPELRKIRGFRGIHIEGFKT--RTFGSVKAFPAKIQNIPCFVIMPERTVYTDVIEIISD------------DRVSVEVYT 220
                                    14        24        34        44        54        64        74        84        94      |  -       114       124   |   134       144       154     | 164       174       184       194    |    -       214      
                                                                                                                          101          114           128 132                         160  |                                 199          212        
                                                                                                                                                                                        163
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  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 Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CTA)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (RIFK_THEAC | Q9HJA6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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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