PDBsum entry 2vbv

Transferase

PDB id: 2vbv

Contents

Protein chains

134 a.a. *

Ligands

CDP ×2

FMN

Metals

_MG ×2

IOD

_CL

Waters ×73

* Residue conservation analysis

PDB id:

2vbv

Name:

Transferase

Title:

Riboflavin kinase mj0056 from methanocaldococcus jannaschii in complex with cdp and fmn

Structure:

Riboflavin kinase. Chain: a, b. Synonym: uncharacterized protein mj0056. Engineered: yes

Source:

Methanococcus jannaschii. Organism_taxid: 2190. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.40Å R-factor: 0.232 R-free: 0.323

Authors:

M.D.Hartmann,M.Ammelburg,S.Djuranovic,J.Martin,A.N.Lupas,K.Zeth

Key ref:

M.Ammelburg et al. (2007). A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels. Structure, 15, 1577-1590. PubMed id: 18073108 DOI: 10.1016/j.str.2007.09.027

Date:

16-Sep-07 Release date: 20-Nov-07

Protein chains

Q60365  (RIFK_METJA) -  Riboflavin kinase from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 132 a.a.

Struc: 134 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.1.161 - CTP-dependent riboflavin kinase.
• Reaction: riboflavin + CTP = CDP + FMN + H⁺

riboflavin + CTP = CDP (Bound ligand (Het Group name = CDP) corresponds exactly) + FMN (Bound ligand (Het Group name = FMN) corresponds exactly) + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.str.2007.09.027

Structure 15:1577-1590 (2007)

PubMed id: 18073108

A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels.

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.

ABSTRACT

Proteins of the cradle-loop barrel metafold are formed by duplication of a conserved betaalphabeta-element, suggesting a common evolutionary origin from an ancestral group of nucleic acid-binding proteins. The basal fold within this metafold, the RIFT barrel, is also found in a wide range of enzymes, whose homologous relationship with the nucleic acid-binding group is unclear. We have characterized a protein family that is intermediate in sequence and structure between the basal group of cradle-loop barrels and one family of RIFT-barrel enzymes, the riboflavin kinases. We report the structure, substrate-binding mode, and catalytic activity for one of these proteins, Methanocaldococcus jannaschii Mj0056, which is an archaeal riboflavin kinase. Mj0056 is unusual in utilizing CTP rather than ATP as the donor nucleotide, and sequence conservation in the relevant residues suggests that this is a general feature of archaeal riboflavin kinases.

Selected figure(s)

Figure 2.
Figure 2. Cluster Map of Mj0065 Homologs
The map, obtained with CLANS (see Experimental Procedures), shows Mj0056 in the context of double-psi barrels (AAA N domains, double-psi barrel enzymes), swapped-hairpin barrels (AbrB superfamily), and RIFT barrels (PhS018 group, riboflavin kinases, riboflavin synthases).

Figure 8.
Figure 8. Structural Comparison of Archaeal and Bacterial/Eukaryotic RFKs
Mj0056-MgCDP-FMN (A) is compared to HsRFK-MgADP-FMN (1Q9S) (B). A superposition of the nucleotide binding sites (C) illustrates how the absence of α1′ in HsRFK accommodates the larger adenosine moiety. The superimposition in (D) shows the FMN binding site, highlighting the structural equivalence of α1 in Mj0056 to the C-terminal extension in HsRFK.

The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 1577-1590) copyright 2007.

Figures were selected by an automated process.