PDBsum entry 2hmf

Transferase

PDB id: 2hmf

Contents

Protein chains

464 a.a. *

Ligands

ADP ×4

ASP ×4

Metals

_MG ×4

Waters ×123

* Residue conservation analysis

PDB id:

2hmf

Name:

Transferase

Title:

Structure of a threonine sensitive aspartokinase from methanococcus jannaschii complexed with mg-adp and aspartate

Structure:

Probable aspartokinase. Chain: a, b, c, d. Synonym: aspartate kinase. Engineered: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.70Å R-factor: 0.243 R-free: 0.276

Authors:

C.R.Faehnle,R.E.Viola

Key ref:

C.R.Faehnle et al. (2006). The initial step in the archaeal aspartate biosynthetic pathway catalyzed by a monofunctional aspartokinase. Acta Crystallograph Sect F Struct Biol Cryst Commun, 62, 962-966. PubMed id: 17012784 DOI: 10.1107/S1744309106038279

Date:

11-Jul-06 Release date: 17-Oct-06

Protein chains

Q57991  (AK_METJA) -  Probable aspartokinase from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 473 a.a.

Struc: 464 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.2.4 - aspartate kinase.
• Pathway: Lysine biosynthesis (early stages)
• Reaction: L-aspartate + ATP = 4-phospho-L-aspartate + ADP

L-aspartate + ATP (Bound ligand (Het Group name = ASP) corresponds exactly) = 4-phospho-L-aspartate + ADP (Bound ligand (Het Group name = ADP) corresponds exactly)

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

reference

DOI no: 10.1107/S1744309106038279

Acta Crystallograph Sect F Struct Biol Cryst Commun 62:962-966 (2006)

PubMed id: 17012784

The initial step in the archaeal aspartate biosynthetic pathway catalyzed by a monofunctional aspartokinase.

C.R.Faehnle, X.Liu, A.Pavlovsky, R.E.Viola.

ABSTRACT

The activation of the beta-carboxyl group of aspartate catalyzed by aspartokinase is the commitment step to amino-acid biosynthesis in the aspartate pathway. The first structure of a microbial aspartokinase, that from Methanococcus jannaschii, has been determined in the presence of the amino-acid substrate L-aspartic acid and the nucleotide product MgADP. The enzyme assembles into a dimer of dimers, with the interfaces mediated by both the N- and C-terminal domains. The active-site functional groups responsible for substrate binding and specificity have been identified and roles have been proposed for putative catalytic functional groups.

Selected figure(s)

Figure 3.
Figure 3 An F[o] - F[c] OMIT map showing the fit of the substrate (L-aspartate) and product (MgADP) to the electron density.

Figure 4.
Figure 4 Expansion of the mjAK structure showing the substrate-binding sites. (a) The amino-acid binding site, with each interaction <3.4 Å annotated. The -carboxyl group of L-aspartate (L-ASP) forms an ion pair with Arg207 and a hydrogen bond with the backbone amide of Gly206 and the side chain of Thr46. The -amino group of L-aspartate interacts electrostatically with the carboxyl group of Glu130. The -carboxyl group, the phosphoryl acceptor, forms hydrogen bonds with the backbone amide of Ser210 and the side chain of Ser40. (b) The nucleotide-binding site. The divalent cation, Mg^2+, forms a bridge between the - and -phosphate groups of ADP. The ribose moiety is bound by interactions with the side chains of Asp231, Asp239 and Arg241, while the adenine ring is positioned through hydrophobic interactions with Val267 as well as a hydrogen bond to the hydroxyl group of Tyr236.

The above figures are reprinted by permission from the IUCr: Acta Crystallograph Sect F Struct Biol Cryst Commun (2006, 62, 962-966) copyright 2006.

Figures were selected by the author.