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PDBsum entry 1q67

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protein Protein-protein interface(s) links
Transcription PDB id
1q67
Jmol
Contents
Protein chains
146 a.a. *
161 a.a. *
Waters ×156
* Residue conservation analysis
PDB id:
1q67
Name: Transcription
Title: Crystal structure of dcp1p
Structure: Decapping protein involved in mRNA degradation- dcp1p. Chain: a, b. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: dcp1. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.30Å     R-factor:   0.227     R-free:   0.268
Authors: M.She,C.J.Decker,Y.Liu,N.Chen,R.Parker,H.Song
Key ref:
M.She et al. (2004). Crystal structure of Dcp1p and its functional implications in mRNA decapping. Nat Struct Mol Biol, 11, 249-256. PubMed id: 14758354 DOI: 10.1038/nsmb730
Date:
12-Aug-03     Release date:   02-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q12517  (DCP1_YEAST) -  mRNA-decapping enzyme subunit 1
Seq:
Struc:
231 a.a.
146 a.a.
Protein chain
Pfam   ArchSchema ?
Q12517  (DCP1_YEAST) -  mRNA-decapping enzyme subunit 1
Seq:
Struc:
231 a.a.
161 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     positive regulation of catalytic activity   4 terms 
  Biochemical function     protein binding     5 terms  

 

 
DOI no: 10.1038/nsmb730 Nat Struct Mol Biol 11:249-256 (2004)
PubMed id: 14758354  
 
 
Crystal structure of Dcp1p and its functional implications in mRNA decapping.
M.She, C.J.Decker, K.Sundramurthy, Y.Liu, N.Chen, R.Parker, H.Song.
 
  ABSTRACT  
 
A major pathway of eukaryotic mRNA turnover begins with deadenylation, followed by decapping and 5'-->3' exonucleolytic degradation. A critical step in this pathway is decapping, which is carried out by an enzyme composed of Dcp1p and Dcp2p. The crystal structure of Dcp1p shows that it markedly resembles the EVH1 family of protein domains. Comparison of the proline-rich sequence (PRS)-binding sites in this family of proteins with Dcp1p indicates that it belongs to a novel class of EVH1 domains. Mapping of the sequence conservation on the molecular surface of Dcp1p reveals two prominent sites. One of these is required for the function of the Dcp1p-Dcp2p complex, and the other, corresponding to the PRS-binding site of EVH1 domains, is probably a binding site for decapping regulatory proteins. Moreover, a conserved hydrophobic patch is shown to be critical for decapping.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal structure of Dcp1p in comparison with EVH1 domains from Mena, Homer, N-WASP and RanBP. (a) Ribbon diagram of Dcp1p with secondary structural elements labeled. Two clusters of conserved residues on opposite concave surfaces (patches 1 and 2) are shown as ball-and-stick models colored by atom type. (b) Structure of the Mena EVH1 domain in complex with an eight-residue peptide (purple) from ActA. (c) Structure of the Homer EVH1 domain in complex with a five-residue peptide (purple) from mGluR. (d) NMR structure of the N-WASP EVH1 domain in complex with WIP peptide (residues 461 -485, purple). Residues 479 -485 are not included in the drawing owing to a lack of resonance assignments. Arg76, the most frequently mutated residue in Wiskott-Aldrich syndrome (WAS) is shown in ball-and-stick form. (e) Structure of the RanBP EVH1 domain in complex with an extended >25-residue polypeptide from Ran (purple). (f) Structure of PH domain from DAPP1/PHISH in complex with Ins(1,3,4,5)P[4]. The bound inositol phosphate is shown in ball-and-stick form. Figures 1 and 5 were produced using MolScript48.
Figure 3.
Figure 3. Molecular surface views of Dcp1p. (a) Surface representation of Dcp1p showing the regions of high to low sequence conservation shared by the eukaryotic Dcp1 proteins, corresponding to a color ramp from red to blue, respectively. The conserved patch 1, corresponding to the PRS-binding site in other EVH1 domains, is shown. Invariant residues are labeled. (b) The conserved patch 2, which is critical for Dcp1p function. Invariant residues are labeled. The coloring scheme is as in a. The view is similar to that in Figure 1a. (c) Molecular surfaces of Dcp1p colored according to residue property, with hydrophobic residues magenta and other residues gray. The hydrophobic patch is marked by a black circle and residues forming the hydrophobic patch on Dcp1p surface are labeled, with conserved residues blue and variant residues black. Figures were produced using GRASP50.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 249-256) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23142987 J.E.Braun, V.Truffault, A.Boland, E.Huntzinger, C.T.Chang, G.Haas, O.Weichenrieder, M.Coles, and E.Izaurralde (2012).
A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5' exonucleolytic degradation.
  Nat Struct Mol Biol, 19, 1324-1331.
PDB code: 2lyd
21070968 M.G.Song, Y.Li, and M.Kiledjian (2010).
Multiple mRNA decapping enzymes in mammalian cells.
  Mol Cell, 40, 423-432.  
19966221 F.Tritschler, J.E.Braun, C.Motz, C.Igreja, G.Haas, V.Truffault, E.Izaurralde, and O.Weichenrieder (2009).
DCP1 forms asymmetric trimers to assemble into active mRNA decapping complexes in metazoa.
  Proc Natl Acad Sci U S A, 106, 21591-21596.
PDB codes: 2wx3 2wx4
19233875 Y.Li, E.S.Ho, S.I.Gunderson, and M.Kiledjian (2009).
Mutational analysis of a Dcp2-binding element reveals general enhancement of decapping by 5'-end stem-loop structures.
  Nucleic Acids Res, 37, 2227-2237.  
18755833 M.Jinek, A.Eulalio, A.Lingel, S.Helms, E.Conti, and E.Izaurralde (2008).
The C-terminal region of Ge-1 presents conserved structural features required for P-body localization.
  RNA, 14, 1991-1998.
PDB code: 2vxg
18280239 M.She, C.J.Decker, D.I.Svergun, A.Round, N.Chen, D.Muhlrad, R.Parker, and H.Song (2008).
Structural basis of dcp2 recognition and activation by dcp1.
  Mol Cell, 29, 337-349.
PDB codes: 2qkl 2qkm
18280238 M.V.Deshmukh, B.N.Jones, D.U.Quang-Dang, J.Flinders, S.N.Floor, C.Kim, J.Jemielity, M.Kalek, E.Darzynkiewicz, and J.D.Gross (2008).
mRNA decapping is promoted by an RNA-binding channel in Dcp2.
  Mol Cell, 29, 324-336.
PDB code: 2jvb
  18971632 S.N.Floor, B.N.Jones, and J.D.Gross (2008).
Control of mRNA decapping by Dcp2: An open and shut case?
  RNA Biol, 5, 189-192.  
19061636 T.M.Franks, and J.Lykke-Andersen (2008).
The control of mRNA decapping and P-body formation.
  Mol Cell, 32, 605-615.  
18039849 Y.Li, M.G.Song, and M.Kiledjian (2008).
Transcript-specific decapping and regulated stability by the human Dcp2 decapping protein.
  Mol Cell Biol, 28, 939-948.  
17429074 D.Teixeira, and R.Parker (2007).
Analysis of P-body assembly in Saccharomyces cerevisiae.
  Mol Biol Cell, 18, 2274-2287.  
17923697 F.Tritschler, A.Eulalio, V.Truffault, M.D.Hartmann, S.Helms, S.Schmidt, M.Coles, E.Izaurralde, and O.Weichenrieder (2007).
A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting.
  Mol Cell Biol, 27, 8600-8611.
PDB codes: 2rm4 2vc8
17878665 L.Deng, T.Kakihara, R.Fukuda, and A.Ohta (2007).
Isolation and characterization of a mutant defective in utilization of exogenous phosphatidylethanolamine in Saccharomyces cerevisiae.
  J Gen Appl Microbiol, 53, 255-258.  
17882262 N.Troffer-Charlier, V.Cura, P.Hassenboehler, D.Moras, and J.Cavarelli (2007).
Functional insights from structures of coactivator-associated arginine methyltransferase 1 domains.
  EMBO J, 26, 4391-4401.
PDB codes: 2oqb 3b3f 3b3g 3b3j
16580207 E.Simon, S.Camier, and B.Séraphin (2006).
New insights into the control of mRNA decapping.
  Trends Biochem Sci, 31, 241-243.  
16341225 M.She, C.J.Decker, N.Chen, S.Tumati, R.Parker, and H.Song (2006).
Crystal structure and functional analysis of Dcp2p from Schizosaccharomyces pombe.
  Nat Struct Mol Biol, 13, 63-70.
PDB code: 2a6t
16395315 S.Bail, and M.Kiledjian (2006).
More than 1 + 2 in mRNA decapping.
  Nat Struct Mol Biol, 13, 7-9.  
17157254 X.Jiao, Z.Wang, and M.Kiledjian (2006).
Identification of an mRNA-decapping regulator implicated in X-linked mental retardation.
  Mol Cell, 24, 713-722.  
15901504 C.Fillman, and J.Lykke-Andersen (2005).
RNA decapping inside and outside of processing bodies.
  Curr Opin Cell Biol, 17, 326-331.  
16199859 L.S.Cohen, C.Mikhli, X.Jiao, M.Kiledjian, G.Kunkel, and R.E.Davis (2005).
Dcp2 Decaps m2,2,7GpppN-capped RNAs, and its activity is sequence and context dependent.
  Mol Cell Biol, 25, 8779-8791.  
16040597 S.Balaji, M.M.Babu, L.M.Iyer, and L.Aravind (2005).
Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains.
  Nucleic Acids Res, 33, 3994-4006.  
15496519 K.E.Baker, and C.Condon (2004).
Under the Tucson sun: a meeting in the desert on mRNA decay.
  RNA, 10, 1680-1691.  
15265035 M.Albrecht, M.Golatta, U.Wüllner, and T.Lengauer (2004).
Structural and functional analysis of ataxin-2 and ataxin-3.
  Eur J Biochem, 271, 3155-3170.  
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.