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PDBsum entry 2dpx

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protein ligands metals Protein-protein interface(s) links
Signaling protein PDB id
2dpx
Jmol
Contents
Protein chains
146 a.a. *
135 a.a. *
Ligands
GDP ×2
Metals
_MG ×2
Waters ×83
* Residue conservation analysis
PDB id:
2dpx
Name: Signaling protein
Title: Crystal structure of human rad gtpase
Structure: Gtp-binding protein rad. Chain: a, b. Fragment: gtpase domain. Synonym: ras associated with diabetes, rad1, rad gtpase. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: rrad, rad. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.214     R-free:   0.240
Authors: A.Yanuar,S.Sakurai,K.Kitano,T.Hakoshima
Key ref: A.Yanuar et al. (2006). Crystal structure of human Rad GTPase of the RGK-family. Genes Cells, 11, 961-968. PubMed id: 16866878
Date:
18-May-06     Release date:   08-Aug-06    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P55042  (RAD_HUMAN) -  GTP-binding protein RAD
Seq:
Struc:
308 a.a.
146 a.a.
Protein chain
Pfam   ArchSchema ?
P55042  (RAD_HUMAN) -  GTP-binding protein RAD
Seq:
Struc:
308 a.a.
135 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     signal transduction   4 terms 
  Biochemical function     GTP binding     1 term  

 

 
Genes Cells 11:961-968 (2006)
PubMed id: 16866878  
 
 
Crystal structure of human Rad GTPase of the RGK-family.
A.Yanuar, S.Sakurai, K.Kitano, T.Hakoshima.
 
  ABSTRACT  
 
Rad (Ras associated with diabetes) is an RGK-family small GTPase that is over-expressed in the skeletal muscle of humans with type II diabetes. Unlike other small GTPases, RGK family members including Rad lack several conserved residues in the GTPase domain. Here, we report the crystal structure of the GTPase domain of human Rad in the GDP-bound form at 1.8 A resolution. The structure revealed unexpected disordered structures of both switches I and II. We showed that the conformational flexibility of both switches is caused by non-conservative substitutions in the G2 and G3 motifs forming the switch cores together with other substitutions in the structural elements interacting with the switches. Glycine-rich sequences of the switches would also contribute to the flexibility. Switch I lacks the conserved phenylalanine that makes non-polar interactions with the guanine base in H-Ras. Instead, water-mediated hydrogen bonding interactions were observed in Rad. The GDP molecule is located at the same position as in H-Ras and adopts a similar conformation as that bound in H-Ras. This similarity seems to be endowed by the conserved hydrogen bonding interactions with the guanine base-recognition loops and the magnesium ion that has a typical octahedral coordination shell identical to that in H-Ras.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18042346 R.N.Correll, C.Pang, D.M.Niedowicz, B.S.Finlin, and D.A.Andres (2008).
The RGK family of GTP-binding proteins: regulators of voltage-dependent calcium channels and cytoskeleton remodeling.
  Cell Signal, 20, 292-300.  
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.