PDBsum entry: 1ex6

Transferase

PDB-id: 1ex6

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PROCHECK

Protein chains

186 a.a. *

Waters ×424

* Residue conservation analysis

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Clefts Calculation

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PDB id:

1ex6

Name:

Transferase

Title:

Crystal structure of unliganded form of guanylate kinase from yeast

Structure:

Guanylate kinase. Chain: a, b. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

UniProt:

Chains A, B: P15454 (KGUA_YEAST)

Seq:

187 a.a.

Struc:

186 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.2.7.4.8   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

ATP + GMP = ADP + GDP (see diagram below)

Resolution:

2.30Å

R-factor:

0.214

R-free:

0.259

Authors:

J.Blaszczyk,X.Ji

Key ref:

J.Blaszczyk et al. (2001). Crystal structure of unligated guanylate kinase from yeast reveals GMP-induced conformational changes.. J Mol Biol, 307, 247-257. [PubMed id: 11243817] [DOI: 10.1006/jmbi.2000.4427]

Date:

01-May-00

Release date:

16-Mar-01

Related entries:

1gky
1gky is the crystal structure of a complex of n-acetylated
guanylate kinase from yeast with gmp
1ex7
1ex7 is the crystal structure of a complex of non-(n-
acetylated) guanylate kinase from yeast with gmp

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Key reference

DOI no: 10.1006/jmbi.2000.4427

J Mol Biol 307:247-257 (2001)

PubMed id: 11243817

Crystal structure of unligated guanylate kinase from yeast reveals GMP-induced conformational changes.

J.Blaszczyk, Y.Li, H.Yan, X.Ji.

ABSTRACT

The crystal structure of guanylate kinase (GK) from yeast (Saccharomyces cerevisiae) with a non-acetylated N terminus has been determined in its unligated form (apo-GK) as well as in complex with GMP (GK.GMP). The structure of apo-GK was solved with multiwavelength anomalous diffraction data and refined to an R-factor of 0.164 (R(free)=0.199) at 2.3 A resolution. The structure of GK.GMP was determined using the crystal structure of GK with an acetylated N terminus as the search model and refined to an R-factor of 0.156 (R(free)=0.245) at 1.9 A. GK belongs to the family of nucleoside monophosphate (NMP) kinases and catalyzes the reversible phosphoryl transfer from ATP to GMP. Like other NMP kinases, GK consists of three dynamic domains: the CORE, LID, and NMP-binding domains. Dramatic movements of the GMP-binding domain and smaller but significant movements of the LID domain have been revealed by comparing the structures of apo-GK and GK.GMP. apo-GK has a much more open conformation than the GK.GMP complex. Systematic analysis of the domain movements using the program DynDom shows that the large movements of the GMP-binding domain involve a rotation around an effective hinge axis approximately parallel with helix 3, which connects the GMP-binding and CORE domains. The C-terminal portion of helix 3, which connects to the CORE domain, has strikingly higher temperature factors in GK.GMP than in apo-GK, indicating that these residues become more mobile upon GMP binding. The results suggest that helix 3 plays an important role in domain movement. Unlike the GMP-binding domain, which moves toward the active center of the enzyme upon GMP binding, the LID domain moves away from the active center and makes the presumed ATP-binding site more open. Therefore, the LID domain movement may facilitate the binding of MgATP. The structure of the recombinant GK.GMP complex superimposes very well with that of the native GK.GMP complex, indicating that N-terminal acetylation does not have significant impact on the three-dimensional structure of GK.

Selected figure(s)

Figure 3.
Figure 3. Dynamic domains in (a) Mol A and (b) Mol B of apo-GK determined by the program DynDom [Hayward and Berendsen 1998]. The CORE and LID domains are blue, the GMP-binding domain is red, and the residues that are involved in the interdomain motions are green. The long black arrow is the effective hinge axis, with the arrow indicating direction of the rotation of the GMP-binding domain by the right-hand rule [Hayward and Berendsen 1998].

Figure 4.
Figure 4. Superposition of the GMP-binding sites in apo-Mol A (thin continuous line), apo-Mol B (thin broken line), and GK·GMP (thick continuous line). The superposition was optimized for the C^a atoms of the GMP-binding domain. For clarity, only the side-chains of the polar residues are shown, among which Asp100 is from the CORE domain.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 307, 247-257) copyright 2001.

Figures were selected by the author.