PDBsum entry 1dvr

Transferase (phosphotransferase)

PDB id: 1dvr

Contents

Protein chains

220 a.a. *

Ligands

ATF ×2

Waters ×161

* Residue conservation analysis

PDB id:

1dvr

Name:

Transferase (phosphotransferase)

Title:

Structure of a mutant adenylate kinase ligated with an atp-analogue showing domain closure over atp

Structure:

Adenylate kinase. Chain: a, b. Synonym: atp:amp-phosphotransferase, myokinase. Engineered: yes. Mutation: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Cellular_location: cytosol. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.36Å R-factor: 0.191

Authors:

G.J.Schlauderer,G.E.Schulz

Key ref:

G.J.Schlauderer et al. (1996). Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP. J Mol Biol, 256, 223-227. PubMed id: 8594191 DOI: 10.1006/jmbi.1996.0080

Date:

14-Dec-95 Release date: 03-Apr-96

Protein chains

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

Seq: 222 a.a.

Struc: 220 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

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

AMP + ATP = 2 × ADP (Bound ligand (Het Group name = ATF) matches with 76.47% similarity)

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

reference

DOI no: 10.1006/jmbi.1996.0080

J Mol Biol 256:223-227 (1996)

PubMed id: 8594191

Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP.

G.J.Schlauderer, K.Proba, G.E.Schulz.

ABSTRACT

Structural studies on unligated and ligated adenylate kinases have shown that two domains, LID and NMPbind, close over the bound substrates, ATP and AMP, respectively. These motions can be, but need not be independent from each other. Up to now, the known structures display only the states "both domains open", "both closed" and "NMP bind closed". In spite of numerous cocrystallization attempts with ATP, a crystalline state "LID closed" has not yet been produced. These experiences suggested that LID closure depends on a bound AMP molecule, in contrast to enzyme kinetic studies indicating a random-bi-bi mechanism. Using an inactive mutant of yeast adenylate kinase together with the ATP analogue AMPPCF2P, however, we have now crystallized an adenylate kinase in the LID closed state. The structure was established at 2.36 A resolution; it indicates that the domain motions occur largely independent from each other in agreement with the kinetic studies. As a side-result, we report the protein environment of the fluorine atoms of the bound ATP analogue.

Selected figure(s)

Figure 1.
Figure 1. Superposition of molecule I of AKyst (D89V, R165I):AMPPCF2 P (thick lines, some residues labeled) with the complex AKyst :Ap5A:Mg (thin lines, Mg 2+ marked by a cross) on the CORE domains. Both LID domains are closed whereas the NMPbind domain conformations differ. The NMPbind domain of the reported structure is open.

Figure 3.
Figure 3. Local symmetry in the crystal structure of AK yst(D89V, R165I):AMPPCF2P. The stereoview is along the non-crystallographic 2-fold axis and approximately the same as in Figure 1. Some residues are labeled. The side-chains of the mutated residues as well as AMPPCF2P are depicted and emphasized in both molecules.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 256, 223-227) copyright 1996.

Figures were selected by an automated process.