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PDBsum entry 1n6i

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protein ligands metals links
Protein transport PDB id
1n6i
Jmol
Contents
Protein chain
167 a.a. *
Ligands
GDP
BME
Metals
_MG
Waters ×236
* Residue conservation analysis
PDB id:
1n6i
Name: Protein transport
Title: Crystal structure of human rab5a a30p mutant complex with gdp
Structure: Ras-related protein rab-5a. Chain: a. Fragment: gtpase domain. Synonym: rab5a. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.60Å     R-factor:   0.178     R-free:   0.214
Authors: G.Zhu,J.Liu,S.Terzyan,P.Zhai,G.Li,X.C.Zhang
Key ref:
G.Zhu et al. (2003). High resolution crystal structures of human Rab5a and five mutants with substitutions in the catalytically important phosphate-binding loop. J Biol Chem, 278, 2452-2460. PubMed id: 12433916 DOI: 10.1074/jbc.M211042200
Date:
11-Nov-02     Release date:   27-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20339  (RAB5A_HUMAN) -  Ras-related protein Rab-5A
Seq:
Struc:
215 a.a.
167 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein transport   2 terms 
  Biochemical function     GTP binding     1 term  

 

 
DOI no: 10.1074/jbc.M211042200 J Biol Chem 278:2452-2460 (2003)
PubMed id: 12433916  
 
 
High resolution crystal structures of human Rab5a and five mutants with substitutions in the catalytically important phosphate-binding loop.
G.Zhu, J.Liu, S.Terzyan, P.Zhai, G.Li, X.C.Zhang.
 
  ABSTRACT  
 
GTPase domain crystal structures of Rab5a wild type and five variants with mutations in the phosphate-binding loop are reported here at resolutions up to 1.5 A. Of particular interest, the A30P mutant was crystallized in complexes with GDP, GDP+AlF(3), and authentic GTP, respectively. The other variant crystals were obtained in complexes with a non-hydrolyzable GTP analog, GppNHp. All structures were solved in the same crystal form, providing an unusual opportunity to compare structures of small GTPases with different catalytic rates. The A30P mutant exhibits dramatically reduced GTPase activity and forms a GTP-bound complex stable enough for crystallographic analysis. Importantly, the A30P structure with bound GDP plus AlF(3) has been solved in the absence of a GTPase-activating protein, and it may resemble that of a transition state intermediate. Conformational changes are observed between the GTP-bound form and the transition state intermediate, mainly in the switch II region containing the catalytic Gln(79) residue and independent of A30P mutation-induced local alterations in the P-loop. The structures suggest an important catalytic role for a P-loop backbone amide group, which is eliminated in the A30P mutant, and support the notion that the transition state of GTPase-mediated GTP hydrolysis is of considerable dissociative character.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. A30R compared with WT. Crystal structures of A30R ( blue) and WT (red) are superimposed, and their catalytic sites are shown. Also superimposed are the F[obs(A30R)] F[obs(WT]) difference electron densities contoured at 3.5 , with positive density colored in cyan and negative in pink. These densities represent the most significant features in the entire difference map and are typical for all mutants of non-proline substitutions reported here. Mg2+ and ordered water molecules are shown as large and small crosses, respectively.
Figure 3.
Fig. 3. Structures of A30P mutant. A, reduce structural comparison between GppNHp·WT and GTP·A30P. WT is shown in red and A30P in blue. The water hydrogen-bond network around the active site and Mg2+ coordination are shown in dashed lines. Mg2+ and ordered water molecules are shown as large and small crosses, respectively. B, structural comparison among the three A30P complexes. The active sites of GTP- (blue), (GDP+AlF[3])- (red), and GDP- (yellow) forms of A30P are superimposed on each other. C, active site structure of the (GDP+AlF[3])·A30P complex. 2F[obs] F[calc] map was contoured at 1.0 and superimposed with a ball-and-stick model of the final refined structure. Carbon (yellow), nitrogen (blue), oxygen (red), phosphate (white), aluminum (cyan), fluoride (magenta), and magnesium (green) ions are colored, respectively. The coordination of both Mg2+ and Al3+ (except the Al-F bonds) are shown in thin lines. Orientations are the same as that of Fig. 2.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 2452-2460) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20649471 J.Heo (2011).
Redox control of GTPases: from molecular mechanisms to functional significance in health and disease.
  Antioxid Redox Signal, 14, 689-724.  
20534488 A.Mishra, S.Eathiraj, S.Corvera, and D.G.Lambright (2010).
Structural basis for Rab GTPase recognition and endosome tethering by the C2H2 zinc finger of Early Endosomal Autoantigen 1 (EEA1).
  Proc Natl Acad Sci U S A, 107, 10866-10871.
PDB code: 3mjh
20400571 B.Huang, H.Wu, N.Hao, F.Blombach, J.van der Oost, X.Li, X.C.Zhang, and Z.Rao (2010).
Functional study on GTP hydrolysis by the GTP-binding protein from Sulfolobus solfataricus, a member of the HflX family.
  J Biochem, 148, 103-113.
PDB codes: 3kxi 3kxk 3kxl
19064930 A.Korostelev, H.Asahara, L.Lancaster, M.Laurberg, A.Hirschi, J.Zhu, S.Trakhanov, W.G.Scott, and H.F.Noller (2008).
Crystal structure of a translation termination complex formed with release factor RF2.
  Proc Natl Acad Sci U S A, 105, 19684-19689.
PDB codes: 3f1e 3f1f 3f1g 3f1h
19081051 G.Nimrod, M.Schushan, D.M.Steinberg, and N.Ben-Tal (2008).
Detection of functionally important regions in "hypothetical proteins" of known structure.
  Structure, 16, 1755-1763.  
17581628 G.Zhu, J.Chen, J.Liu, J.S.Brunzelle, B.Huang, N.Wakeham, S.Terzyan, X.Li, Z.Rao, G.Li, and X.C.Zhang (2007).
Structure of the APPL1 BAR-PH domain and characterization of its interaction with Rab5.
  EMBO J, 26, 3484-3493.
PDB codes: 2q12 2q13
16790928 I.Garcia-Saez, S.Tcherniuk, and F.Kozielski (2006).
The structure of human neuronal Rab6B in the active and inactive form.
  Acta Crystallogr D Biol Crystallogr, 62, 725-733.
PDB codes: 2fe4 2ffq
15468317 A.Golovin, D.Dimitropoulos, T.Oldfield, A.Rachedi, and K.Henrick (2005).
MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites.
  Proteins, 58, 190-199.  
15378032 G.Zhu, P.Zhai, J.Liu, S.Terzyan, G.Li, and X.C.Zhang (2004).
Structural basis of Rab5-Rabaptin5 interaction in endocytosis.
  Nat Struct Mol Biol, 11, 975-983.
PDB codes: 1tu3 1tu4
14636058 P.Zhai, X.He, J.Liu, N.Wakeham, G.Zhu, G.Li, J.Tang, and X.C.Zhang (2003).
The interaction of the human GGA1 GAT domain with rabaptin-5 is mediated by residues on its three-helix bundle.
  Biochemistry, 42, 13901-13908.  
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. Where a reference describes a PDB structure, the PDB code is shown on the right.