PDBsum entry 3ch4

Transferase

PDB id: 3ch4

Contents

Protein chain

188 a.a. *

Ligands

SO4 ×2

MPD ×2

Waters ×148

* Residue conservation analysis

PDB id:

3ch4

Name:

Transferase

Title:

The crystal structure of human phosphomavelonate kinase at 1.8 a resolution

Structure:

Phosphomevalonate kinase. Chain: b. Synonym: pmkase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.76Å R-factor: 0.199 R-free: 0.221

Authors:

D.-C.Liang,Q.Chang,X.-X.Yan,S.-Y.Gu

Key ref:

Q.Chang et al. (2008). Crystal structure of human phosphomevalonate kinase at 1.8 A resolution. Proteins, 73, 254-258. PubMed id: 18618710 DOI: 10.1002/prot.22151

Date:

07-Mar-08 Release date: 29-Jul-08

Protein chain

Q15126  (PMVK_HUMAN) -  Phosphomevalonate kinase from Homo sapiens

Seq: 192 a.a.

Struc: 188 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.4.2 - phosphomevalonate kinase.
• Pathway: Terpenoid biosynthesis
• Reaction: (R)-5-phosphomevalonate + ATP = (R)-5-diphosphomevalonate + ADP

(R)-5-phosphomevalonate (Bound ligand (Het Group name = MPD) matches with 46.67% similarity) + ATP = (R)-5-diphosphomevalonate + ADP

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

reference

DOI no: 10.1002/prot.22151

Proteins 73:254-258 (2008)

PubMed id: 18618710

Crystal structure of human phosphomevalonate kinase at 1.8 A resolution.

Q.Chang, X.X.Yan, S.Y.Gu, J.F.Liu, D.C.Liang.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. A: Stereo ribbon representation of hPMK. The different regions of the enzyme are color-coded. CORE region is shown in magenta, LID region in green, and substrate binding region in light brown. MPD (cyan) and sulfate ions (orange) are shown in stick models. The P-loop is shown in dark blue. B: Stereo ribbon representation of the superposition of DNK (deoxynucleoside monophosphate kinase from Bacteriophage T4, PDB: 1dek) with hPMK. DNK is shown in yellow and PMK in purple.

Figure 2.
Figure 2. A: A superimposed view of the ATP binding site of sulfate-bound PMK (purple), ATP-bound GntK (orange), and ATP-bound DCK (green). The superimposition is based on C atoms of the P-loop, helix 1 and strand 1. ATP, MPD and sulfate ion are shown in stick models. B: The interactions with the bounded sulfate ion and the interactions between residues located in the P-loop and LID region. The sulfate ion (SO[4]) and correlative residues are represented by stick structures, and the remainder of the structure is shown in cartoon representation. Carbon atoms are colored in purple, oxygen atoms in red, nitrogen atoms in blue and the sulfur atom is yellow. Hydrogen bond pairs are connected with green dashed lines. C: Electrostatic surface representation of hPMK with the transparent ribbon presentation. Red represents a negative charge, and blue represents a positive charge. MPD and sulfate ion are represented by sticks. The ATP-binding site is the region within the cyan ellipse, and the substrate-binding site is the region within the white rectangle. An enlarged view of the detailed putative substrate-binding site is shown on the right, and the conserved residues that may interact with mevalonate 5-phosphate are shown by stick structures.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 73, 254-258) copyright 2008.