PDBsum entry 3ec1

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Hydrolase, signaling protein PDB id
Protein chains
311 a.a. *
GDP ×2
Waters ×335
* Residue conservation analysis
PDB id:
Name: Hydrolase, signaling protein
Title: Structure of yqeh gtpase from geobacillus stearothermophilus (an atnos1 / atnoa1 ortholog)
Structure: Yqeh gtpase. Chain: a, b. Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Strain: atcc 12980. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.36Å     R-factor:   0.254     R-free:   0.287
Authors: J.Sudhamsu,B.R.Crane
Key ref:
J.Sudhamsu et al. (2008). The structure of YqeH. An AtNOS1/AtNOA1 ortholog that couples GTP hydrolysis to molecular recognition. J Biol Chem, 283, 32968-32976. PubMed id: 18801747 DOI: 10.1074/jbc.M804837200
28-Aug-08     Release date:   21-Oct-08    
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Protein chains
Pfam   ArchSchema ?
D0VWU7  (D0VWU7_GEOSE) -  YqeH GTPase
369 a.a.
311 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     GTP binding     1 term  


DOI no: 10.1074/jbc.M804837200 J Biol Chem 283:32968-32976 (2008)
PubMed id: 18801747  
The structure of YqeH. An AtNOS1/AtNOA1 ortholog that couples GTP hydrolysis to molecular recognition.
J.Sudhamsu, G.I.Lee, D.F.Klessig, B.R.Crane.
AtNOS1/AtNOA1 was identified as a nitric oxide-generating enzyme in plants, but that function has recently been questioned. To resolve issues surrounding AtNOA1 activity, we report the biochemical properties and a 2.36 A resolution crystal structure of a bacterial AtNOA1 ortholog (YqeH). Geobacillus YqeH fused to a putative AtNOA1 leader peptide complements growth and morphological defects of Atnoa1 mutant plants. YqeH does not synthesize nitric oxide from L-arginine but rather hydrolyzes GTP. The YqeH structure reveals a circularly permuted GTPase domain and an unusual C-terminal beta-domain. A small N-terminal domain, disordered in the structure, binds zinc. Structural homology among the C-terminal domain, the RNA-binding regulator TRAP, and the hypoxia factor pVHL define a recognition module for peptides and nucleic acids. TRAP residues important for RNA binding are conserved by the YqeH C-terminal domain, whose positioning is coupled to GTP hydrolysis. YqeH and AtNOA1 probably act as G-proteins that regulate nucleic acid recognition and not as nitric-oxide synthases.
  Selected figure(s)  
Figure 1.
Crystal structure of GsYqeH. A, the CPG domain (right) has a central seven-stranded β-sheet surrounded by α-helices and binds GDP, which is exposed to the solvent on one side. The C-terminal domain (left) has a 2-fold pseudosymmetric β-fold. B, alternate view of the C-terminal domain. The domain starts (bottom) with a 3[10]-helix (dark orange), followed by a coil (purple), α-helix (purple), five β-strands (blue), a 3[10]-helix (yellow), an α-helix (magenta), coil (magenta), and five β-strands (green).
Figure 4.
GTP hydrolysis may change orientation of C-terminal domain. Superpositions the CPG domains of GsYqeH (blue) and BsYlqF (pink) with the C-terminal domains of either BsYlqF (A) or GsYqeH (B) removed for clarity. Comparison of GTP-bound YlqF and GDP-bound YqeH indicates that GTP binding displaces the conserved Ile from the phosphate pocket and thereby reorients the C-terminal domain.
  The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 32968-32976) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21071678 N.Pauly, C.Ferrari, E.Andrio, D.Marino, S.Piardi, R.Brouquisse, E.Baudouin, and A.Puppo (2011).
MtNOA1/RIF1 modulates Medicago truncatula-Sinorhizobium meliloti nodule development without affecting its nitric oxide content.
  J Exp Bot, 62, 939-948.  
  20944210 A.Andreeva, and A.G.Murzin (2010).
Structural classification of proteins and structural genomics: new insights into protein folding and evolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1190-1197.  
20376346 B.Anand, P.Surana, and B.Prakash (2010).
Deciphering the catalytic machinery in 30S ribosome assembly GTPase YqeH.
  PLoS One, 5, e9944.  
20456051 H.Liu, E.Lau, M.P.Lam, H.Chu, S.Li, G.Huang, P.Guo, J.Wang, L.Jiang, I.K.Chu, C.Lo, and Y.Tao (2010).
OsNOA1/RIF1 is a functional homolog of AtNOA1/RIF1: implication for a highly conserved plant cGTPase essential for chloroplast function.
  New Phytol, 187, 83.  
19540197 B.Anand, P.Surana, S.Bhogaraju, S.Pahari, and B.Prakash (2009).
Circularly permuted GTPase YqeH binds 30S ribosomal subunit: Implications for its role in ribosome assembly.
  Biochem Biophys Res Commun, 386, 602-606.  
19423572 B.Zybailov, G.Friso, J.Kim, A.Rudella, V.R.Rodríguez, Y.Asakura, Q.Sun, and K.J.van Wijk (2009).
Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism.
  Mol Cell Proteomics, 8, 1789-1810.  
19575570 R.A.Britton (2009).
Role of GTPases in bacterial ribosome assembly.
  Annu Rev Microbiol, 63, 155-176.  
19103604 T.Tang, B.Zheng, S.H.Chen, A.N.Murphy, K.Kudlicka, H.Zhou, and M.G.Farquhar (2009).
hNOA1 interacts with complex I and DAP3 and regulates mitochondrial respiration and apoptosis.
  J Biol Chem, 284, 5414-5424.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.