PDBsum entry 2bef

Phosphotransferase

PDB id: 2bef

Contents

Protein chains

150 a.a. *

Ligands

BEF-ADP ×3

Metals

_MG ×3

Waters ×220

* Residue conservation analysis

PDB id:

2bef

Name:

Phosphotransferase

Title:

Crystal structure of ndp kinase complexed with mg, adp, and bef3

Structure:

Nucleoside diphosphate kinase. Chain: a, b, c. Engineered: yes. Other_details: adp, bef3, mg++

Source:

Dictyostelium discoideum. Organism_taxid: 44689. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.30Å R-factor: 0.193

Authors:

Y.W.Xu,J.Cherfils

Key ref:

Y.W.Xu et al. (1997). AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP. Proc Natl Acad Sci U S A, 94, 3579-3583. PubMed id: 9108019 DOI: 10.1073/pnas.94.8.3579

Date:

26-May-98 Release date: 12-Aug-98

Protein chains

P22887  (NDKC_DICDI) -  Nucleoside diphosphate kinase, cytosolic from Dictyostelium discoideum

Seq: 155 a.a.

Struc: 150 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.4.6 - nucleoside-diphosphate kinase.
• Reaction:
  1. a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP
  2. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP

ribonucleoside 5'-diphosphate + ATP = ribonucleoside 5'-triphosphate + ADP (Bound ligand (Het Group name = ADP) corresponds exactly)

2'-deoxyribonucleoside 5'-diphosphate + ATP = 2'-deoxyribonucleoside 5'-triphosphate + ADP (Bound ligand (Het Group name = ADP) corresponds exactly)

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

reference

DOI no: 10.1073/pnas.94.8.3579

Proc Natl Acad Sci U S A 94:3579-3583 (1997)

PubMed id: 9108019

AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP.

Y.W.Xu, S.Moréra, J.Janin, J.Cherfils.

ABSTRACT

Nucleoside diphosphate kinase reversibly transfers the gamma-phosphate of ATP onto its active site histidine. We have investigated the transition state of histidine phosphorylation with the high-resolution crystal structures of the enzyme from Dictyostelium discoideum with MgADP and either aluminium or beryllium fluoride. The bound aluminium fluoride species is the neutral species AlF3 and not the more common AlF4-. AlF3 forms a trigonal bipyramid that makes it an accurate analog of the transition state of the gamma-phosphate of ATP undergoing transfer to the catalytic histidine. Its axial ligands are a histidine nitrogen and a beta-phosphate oxygen. Beryllium fluoride also binds at the same position and with the same ligands but in a tetrahedral geometry resembling the Michaelis complex rather than the transition state. The two x-ray structures show explicit enzyme-substrate interactions that discriminate between the ground and the transition states of the reaction. They also illustrate the partially dissociative geometry of the transition state of phosphoryl transfer and demonstrate the potential applications of metallofluorides for the study of kinase mechanisms.

Selected figure(s)

Figure 1.
Fig. 1. Simulated annealing F[o]-F[c] omit maps contoured at 3.5 showing ADP (to the left) and His-122 (to the right). (A) AlF[3] omit map at 2.0-Å resolution. Al3+ (green) in trigonal bipyramidal configuration is shown coordinating to three equatorial fluorines (orange) and with partial bonds to ADP O[7] and to His-122 N . Mg2+ (white) has an octahedral geometry, with a tridendate coordination to the - and -phosphates and a fluorine atom and three water molecules (red) as additional ligands. (B) BeF[3]^ omit map at 2.3-Å resolution. Be^2+ (green) is modeled in a tetrahedral geometry, with three fluorines and O[7] as the fourth ligand. An alternative configuration for Be^2+ has His-122 N as the fourth ligand.

Figure 2.
Fig. 2. Schematic representation of NDPK-nucleotide interactions. (A) ADP-AlF[3] from the x-ray structure. (B) ADP-BeF[3]^ with Be^2+ modeled at the -phosphate O[7] as in Fig. 1B. In all cases, there^ is a short hydrogen bond between the 3 hydroxyl of the ribose^ and the -phosphate O[7].

Figures were selected by an automated process.