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PDBsum entry 2k5u
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Signaling protein PDB id
2k5u

 

 

 

 

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Contents
Protein chain
181 a.a. *
Ligands
GDP
* Residue conservation analysis
PDB id:
2k5u
Name: Signaling protein
Title: Solution structure of myirstoylated yeast arf1 protein, gdp-bound
Structure: Adp-ribosylation factor 1. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Rat. Organism_taxid: 4932. Gene: arf1. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 16 models
Authors: J.Prestegard,Y.Liu
Key ref:
Y.Liu et al. (2009). Structure and Membrane Interaction of Myristoylated ARF1. Structure, 17, 79-87. PubMed id: 19141284 DOI: 10.1016/j.str.2008.10.020
Date:
30-Jun-08     Release date:   27-Jan-09    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11076  (ARF1_YEAST) -  ADP-ribosylation factor 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		181 a.a.
181 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
DOI no: 10.1016/j.str.2008.10.020 Structure 17:79-87 (2009)
PubMed id: 19141284  
 
 
Structure and Membrane Interaction of Myristoylated ARF1.
Y.Liu, R.A.Kahn, J.H.Prestegard.
 
  ABSTRACT  
 
ADP-ribosylation factors (ARFs) are small (21 kDa), monomeric GTPases that are important regulators of membrane traffic. When membrane bound, they recruit soluble adaptors to membranes and trigger the assembly of coating complexes involved in cargo selection and vesicular budding. N-myristoylation is a conserved feature of all ARF proteins that is required for its biological functions, although the mechanism(s) by which the myristate acts in ARF functions is not fully understood. Here we present the structure of a myristoylated ARF1 protein, determined by solution NMR methods, and an assessment of the influence of myristoylation on association of ARF1.GDP and ARF1.GTP with lipid bilayers. A model in which myristoylation contributes to both the regulation of guanine nucleotide exchange and stable membrane association is supported.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. ^15N-^1H HSQC Spectra of myr(+)- and myr(−)-yARF1·GDP
myr(+)- and myr(−)-yARF1·GDP are shown in blue and red, respectively. Blown-up views of chemical shift perturbed residues are displayed on the bottom. 		Figure 2.
Figure 2. Structure of Myristoylated yARF1 and Comparisons to Related Structures
(A) Overlap of 15 accepted myr(+)-yARF1·GDP structures out of 100 trials. GDP is shown in blue and myristoyl is in purple.
(B) The myristoyl binding pocket with leucines shown in red, isoleucines in blue, tyrosines in cyan, and myristoyl in purple.
(C) The myristoyl binding pocket lies under the N-terminal amphiphilic helix in the myr(−)-hARF·GDP structure (Protein Data Bank ID code 1hur).
(D) The interstrand loop λ3 clashes with the myristoyl chain in the GTP-bound conformation but not in the GDP-bound conformation. The backbone of myr(+)-yARF1·GDP is shown in ivory, myr(−)-hARF1·GDP in blue, and hARF1Δ17·GTP in green. λ3 of all molecules is shown in red, and myristoyl is shown in purple.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2009, 17, 79-87) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21129209 A.F.Neuwald (2010).
Bayesian classification of residues associated with protein functional divergence: Arf and Arf-like GTPases.
  Biol Direct, 5, 66.  
20404920 J.M.Glück, S.Hoffmann, B.W.Koenig, and D.Willbold (2010).
Single vector system for efficient N-myristoylation of recombinant proteins in E. coli.
  PLoS One, 5, e10081.  
21134634 P.Chavrier, and J.Ménétrey (2010).
Toward a structural understanding of arf family:effector specificity.
  Structure, 18, 1552-1558.  
20214751 X.Jian, M.Cavenagh, J.M.Gruschus, P.A.Randazzo, and R.A.Kahn (2010).
Modifications to the C-terminus of Arf1 alter cell functions and protein interactions.
  Traffic, 11, 732-742.  
20506033 Y.Liu, and J.H.Prestegard (2010).
A device for the measurement of residual chemical shift anisotropy and residual dipolar coupling in soluble and membrane-associated proteins.
  J Biomol NMR, 47, 249-258.  
20601958 Y.Liu, R.A.Kahn, and J.H.Prestegard (2010).
Dynamic structure of membrane-anchored Arf*GTP.
  Nat Struct Mol Biol, 17, 876-881.
PDB code: 2ksq
19141275 J.M.Gruschus, P.W.Chen, R.Luo, and P.A.Randazzo (2009).
Journey to the ends of the Arf.
  Structure, 17, 2-4.  
19879269 R.A.Kahn (2009).
Toward a model for Arf GTPases as regulators of traffic at the Golgi.
  FEBS Lett, 583, 3872-3879.  
19729648 T.J.Pucadyil, and S.L.Schmid (2009).
Conserved functions of membrane active GTPases in coated vesicle formation.
  Science, 325, 1217-1220.  
19854177 V.W.Hsu, and J.S.Yang (2009).
Mechanisms of COPI vesicle formation.
  FEBS Lett, 583, 3758-3763.  
19581113 Y.Liu, and J.H.Prestegard (2009).
Measurement of one and two bond N-C couplings in large proteins by TROSY-based J-modulation experiments.
  J Magn Reson, 200, 109-118.  
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.

 

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