PDBsum entry 2aky

Adenylate kinase

PDB id: 2aky

Contents

Protein chain

218 a.a. *

Ligands

AP5

Metals

_MG

Waters ×459

* Residue conservation analysis

PDB id:

2aky

Name:

Adenylate kinase

Title:

High-resolution structures of adenylate kinase from yeast ligated with inhibitor ap5a, showing the pathway of phosphoryl transfer

Structure:

Adenylate kinase. Chain: a. Synonym: atp\:amp phosphotransferase, myokinase. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: red star, milwaukee. Cellular_location: cytosol. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.96Å R-factor: 0.176

Authors:

U.Abele,G.E.Schulz

Key ref:

U.Abele and G.E.Schulz (1995). High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer. Protein Sci, 4, 1262-1271. PubMed id: 7670369 DOI: 10.1002/pro.5560040702

Date:

28-Jul-95 Release date: 14-Nov-95

Protein chain

P07170  (KAD2_YEAST) -  Adenylate kinase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 222 a.a.

Struc: 218 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.7.4.3 - adenylate kinase.
• Reaction: AMP + ATP = 2 ADP

AMP + ATP (Bound ligand (Het Group name = AP5) matches with 54.39% similarity) = 2 × ADP

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

reference

DOI no: 10.1002/pro.5560040702

Protein Sci 4:1262-1271 (1995)

PubMed id: 7670369

High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer.

U.Abele, G.E.Schulz.

ABSTRACT

The structure of adenylate kinase from yeast ligated with the two-substrate-mimicking inhibitor Ap5A and Mg2+ has been refined to 1.96 A resolution. In addition, the refined structure of the same complex with a bound imidazole molecule replacing Mg2+ has been determined at 1.63 A. These structures indicate that replacing Mg2+ by imidazole disturbs the water structure and thus the complex. A comparison with the G-proteins shows that Mg2+ is exactly at the same position with respect to the phosphates. However, although the Mg2+ ligand sphere of the G-proteins is a regular octahedron containing peptide ligands, the reported adenylate kinase has no such ligands and an open octahedron leaving space for the Mg2+ to accompany the transferred phosphoryl group. A superposition of the known crystalline and therefore perturbed phosphoryl transfer geometries in the adenylate kinases demonstrates that all of them are close to the start of the forward reaction with bound ATP and AMP. Averaging all observed perturbed structures gives rise to a close approximation of the transition state, indicating in general how to establish an elusive transition state geometry. The average shows that the in-line phosphoryl transfer is associative, because there is no space for a dissociative metaphosphate intermediate. As a side result, the secondary dipole interaction in the alpha-helices of both protein structures has been quantified.

Selected figure(s)

Figure 4.
Fig. 4. Relationbetweenthelengthsofprimaryandsecondaryhydro- genbonds in a-helicesasreferredtothedonoramdeatposition . The plotcontainsalla-helicalH-bonds(Fig. 3) frombothreportedstruc- tures.Averageangles N,-H,. . .0,-4 and N,-H,. . .0,-3 are 161" and I1 I, respectively.

Figure 6.
Fig. 6. BindingofImandMg2+in AK,,, ligated with Ap,A.Mostresidues andtwowatermoleulesarelabeled. Chaincutsaremarked by dots. A: Posi- tion f Mg2+(dot) in an extendedwater cluster.Detailedenvronment of Mg2+ is showninFigures8Band9. : Bind- ing of s suspended between hetird phosphteandAsp89.Imidazoledis- turbsappreciablythewateretworkat theactivecenter.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1995, 4, 1262-1271) copyright 1995.

Figures were selected by an automated process.