PDBsum entry: 1f5m

Signaling protein

PDB id: 1f5m

Contents

Protein chains

176 a.a. *

Metals

_BR ×9

Waters ×346

* Residue conservation analysis

PDB id:

1f5m

Name:

Signaling protein

Title:

Structure of the gaf domain

Structure:

Gaf. Chain: a, b. Engineered: yes

Source:

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

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.214 R-free: 0.246

Authors:

Y.S.Ho,L.M.Burden,J.H.Hurley

Key ref:

Y.S.Ho et al. (2000). Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor. EMBO J, 19, 5288-5299. PubMed id: 11032796 DOI: 10.1093/emboj/19.20.5288

Date:

15-Jun-00 Release date: 10-Nov-00

Protein chains

P36088  (FRMSR_YEAST) -  Free methionine-R-sulfoxide reductase

Seq: 180 a.a.

Struc: 176 a.a.

Enzyme reactions

• Enzyme class: E.C.1.8.4.14 - L-methionine (R)-S-oxide reductase.
• Reaction: L-methionine + thioredoxin disulfide + H₂O = L-methionine (R)-S-oxide + thioredoxin
• Cofactor: NADPH

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (2 terms)
• Biological process: response to stress (3 terms)
• Biochemical function: protein binding (4 terms)

reference

DOI no: 10.1093/emboj/19.20.5288

EMBO J 19:5288-5299 (2000)

PubMed id: 11032796

Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor.

Y.S.Ho, L.M.Burden, J.H.Hurley.

ABSTRACT

GAF domains are ubiquitous motifs present in cyclic GMP (cGMP)-regulated cyclic nucleotide phosphodiesterases, certain adenylyl cyclases, the bacterial transcription factor FhlA, and hundreds of other signaling and sensory proteins from all three kingdoms of life. The crystal structure of the Saccharomyces cerevisiae YKG9 protein was determined at 1.9 A resolution. The structure revealed a fold that resembles the PAS domain, another ubiquitous signaling and sensory transducer. YKG9 does not bind cGMP, but the isolated first GAF domain of phosphodiesterase 5 binds with K:(d) = 650 nM. The cGMP binding site of the phosphodiesterase GAF domain was identified by homology modeling and site-directed mutagenesis, and consists of conserved Arg, Asn, Lys and Asp residues. The structural and binding studies taken together show that the cGMP binding GAF domains form a new class of cyclic nucleotide receptors distinct from the regulatory domains of cyclic nucleotide-regulated protein kinases and ion channels.

Selected figure(s)

Figure 4.
Figure 4 (A) The buried Cys/His/Asp/Glu pocket of YKG9 is compared with (B), the chromophore binding site of photoactive yellow protein. (C and D) The same images as (A) and (B) in a surface representation with basic residues colored blue, acidic red, hydrophobic orange and others gray. In (C) and (D) the surface is removed for a portion of the 3– 4 in YKG9 and the equivalent region of photoactive yellow protein in order to show the underlying cavities.

Figure 5.
Figure 5 Similarity between (A) YKG9 and (B) profilin, and (C) YKG9 and (D) photoactive yellow protein. Regions that can be superimposed within 3.0 Å are colored red.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 5288-5299) copyright 2000.

Figures were selected by the author.