2VBT - JenaLib

Title :   RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH CDP AND PO4

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 :   2.70

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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:14 , GLY A:16 , GLY A:18 , ARG A:19 , LYS A:33 , TYR A:40 , GLY A:42 , THR A:43 , LEU A:44 , MET A:112 , LYS A:113 , LEU A:114 , ARG A:115 , NA A:1138 , PO4 A:1139 , HOH A:2030	BINDING SITE FOR RESIDUE CDP A1137
2	AC2	SOFTWARE	THR A:43 , ASN A:45 , CDP A:1137 , PO4 A:1139	BINDING SITE FOR RESIDUE NA A1138
3	AC3	SOFTWARE	LEU A:15 , GLY A:16 , GLU A:17 , ASN A:45 , GLU A:63 , HIS A:101 , CDP A:1137 , NA A:1138 , HOH A:2031	BINDING SITE FOR RESIDUE PO4 A1139

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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)
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Chain A from PDB  Type:PROTEIN  Length:136
 aligned with RIFK_METJA | Q60365 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:136
                                1                                                                                                                                   
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126      
           RIFK_METJA     - ----MIIEGEVVSGLGEGRYFLSLPPYKEIFKKILGFEPYEGTLNLKLDREFDINKFKYIETEDFEFNGKRFFGVKVLPIKILIGNKKIDGAIVVPKKTYHSSEIIEIIAPMKLREQFNLKDGDVIKILIKGDKDE 132
               SCOP domains d2vbta_ A: CTP-dependent riboflavin kinase, Rfk                                                                                          SCOP domains
               CATH domains --2vbtA01 A:3-132 Riboflavin kinase-like                                                                                            ---- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....hhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhh..ee...eee..eee..eeeeeeeeee..eeeeeeeeee........eeeee...hhhhhhh.....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vbt A   1 MVKLMIIEGEVVSGLGEGRYFLSLPPYKEIFKKILGFEPYEGTLNLKLDREFDINKFKYIETEDFEFNGKRFFGVKVLPIKILIGNKKIDGAIVVPKKTYHSSEIIEIIAPMKLREQFNLKDGDVIKILIKGDKDE 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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)

CATH Domains (1, 1)

Pfam Domains (0, 0)

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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