PDBsum entry: 1ohb

Kinase

PDB id: 1ohb

Contents

Protein chain

258 a.a. *

Ligands

SO4

ADP

ACT

Waters ×137

* Residue conservation analysis

PDB id:

1ohb

Name:

Kinase

Title:

Acetylglutamate kinase from escherichia coli complexed with adp and sulphate

Structure:

Acetylglutamate kinase. Chain: a. Synonym: NAG kinase, agk, n-acetyl-l-glutamate 5-phosphotransferase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: bl21(de3). Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.9Å R-factor: 0.194 R-free: 0.221

Authors:

F.Gil-Ortiz,S.Ramon-Maiques,I.Fita,V.Rubio

Key ref:

F.Gil-Ortiz et al. (2003). The course of phosphorus in the reaction of N-acetyl-L-glutamate kinase, determined from the structures of crystalline complexes, including a complex with an AlF(4)(-) transition state mimic. J Mol Biol, 331, 231-244. PubMed id: 12875848 DOI: 10.1016/S0022-2836(03)00716-2

Date:

23-May-03 Release date: 31-Jul-03

Protein chain

P0A6C8  (ARGB_ECOLI) -  Acetylglutamate kinase

Seq: 258 a.a.

Struc: 258 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.2.8 - Acetylglutamate kinase.
• Pathway: Ornithine Biosynthesis
• Reaction: ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamate 5-phosphate

ATP + N-acetyl-L-glutamate = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + N-acetyl-L-glutamate 5-phosphate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: cellular amino acid biosynthetic process (2 terms)
• Biochemical function: nucleotide binding (5 terms)

reference

DOI no: 10.1016/S0022-2836(03)00716-2

J Mol Biol 331:231-244 (2003)

PubMed id: 12875848

The course of phosphorus in the reaction of N-acetyl-L-glutamate kinase, determined from the structures of crystalline complexes, including a complex with an AlF(4)(-) transition state mimic.

F.Gil-Ortiz, S.Ramón-Maiques, I.Fita, V.Rubio.

ABSTRACT

N-Acetyl-L-glutamate kinase (NAGK), the structural paradigm of the enzymes of the amino acid kinase family, catalyzes the phosphorylation of the gamma-COO(-) group of N-acetyl-L-glutamate (NAG) by ATP. We determine here the crystal structures of NAGK complexes with MgADP, NAG and the transition-state analog AlF(4)(-); with MgADP and NAG; and with ADP and SO(4)(2-). Comparison of these structures with that of the MgAMPPNP-NAG complex allows to delineate three successive steps during phosphoryl transfer: at the beginning, when the attacking and leaving O atoms and the P atom are imperfectly aligned and the distance between the attacking O atom and the P atom is 2.8A; midway, at the bipyramidal intermediate, with nearly perfect alignment and a distance of 2.3A; and, when the transfer is completed. The transfer occurs in line and is strongly associative, with Lys8 and Lys217 stabilizing the transition state and the leaving group, respectively, and with Lys61, in contrast with an earlier proposal, not being involved. Three water molecules found in all the complexes play, together with Asp162 and the Mg, crucial structural roles. Two glycine-rich loops (beta1-alphaA and beta2-alphaB) are also very important, moving in the different complexes in concert with the ligands, to which they are hydrogen-bonded, either locking them in place for reaction or stabilizing the transition state. The active site is too narrow to accommodate the substrates without compressing the reacting groups, and this compressive strain appears a crucial component of the catalytic mechanism of NAGK, and possibly of other enzymes of the amino acid kinase family such as carbamate kinase. Initial binding of the two substrates would require a different enzyme conformation with a wider active site, and the energy of substrate binding would be used to change the conformation of the active center, causing substrate strain towards the transition state.

Selected figure(s)

Figure 4.
Figure 4. 2F[obs] -F[calc] maps containing ball-and-stick models of the groups involved in phosphoryl group transfer in the complexes with MgADP-AlF[4]^ --NAG (a), MgAMPPNP-NAG (b) and MgADP-NAG (c). In the MgADP-NAG complex two water molecules occupying an intermediate position between ADP and NAG are also represented as cyan spheres. The indicated interatomic distances and angles are given.

Figure 5.
Figure 5. Stereoview ball-and-stick representation of the phosphoryl group transfer site in the NAGK complexes with MgAMPPNP-NAG (a), MgADP-AlF[4]^ --NAG (b), MgADP-NAG (c) and ADP-SO[4]^2 - (d). Of the ligands only the polyphosphate chain of the nucleotide and the g-carboxylate group of NAG are represented. Mg ion and water molecules are drawn as purple and cyan spheres, respectively. Nearby protein residues are shown in thinner trace. Hydrogen bonds and coordination bonds with Mg are shown as red broken lines, indicating the interatomic distances in Å. In (a) the interatomic distance between the attacking O atom of NAG and the g-P atom is represented with a blue broken line. AlF[4]^ - is shown in green.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 331, 231-244) copyright 2003.

Figures were selected by an automated process.