spacer
spacer

PDBsum entry 2e1e

Go to PDB code: 
protein metals links
Hydrolase PDB id
2e1e
Jmol
Contents
Protein chain
94 a.a. *
Metals
_CL
Waters ×29
* Residue conservation analysis
PDB id:
2e1e
Name: Hydrolase
Title: Crystal structure of the hrdc domain of human werner syndrom wrn
Structure: Werner syndrome atp-dependent helicase. Chain: a. Fragment: hrdc domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Monomer (from PQS)
Resolution:
2.30Å     R-factor:   0.253     R-free:   0.279
Authors: K.Kitano,N.Yoshihara,T.Hakoshima
Key ref:
K.Kitano et al. (2007). Crystal structure of the HRDC domain of human Werner syndrome protein, WRN. J Biol Chem, 282, 2717-2728. PubMed id: 17148451 DOI: 10.1074/jbc.M610142200
Date:
25-Oct-06     Release date:   12-Dec-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q14191  (WRN_HUMAN) -  Werner syndrome ATP-dependent helicase
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1432 a.a.
94 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.6.4.12  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
ATP
+ H(2)O
= ADP
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     cellular metabolic process   1 term 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M610142200 J Biol Chem 282:2717-2728 (2007)
PubMed id: 17148451  
 
 
Crystal structure of the HRDC domain of human Werner syndrome protein, WRN.
K.Kitano, N.Yoshihara, T.Hakoshima.
 
  ABSTRACT  
 
Werner syndrome is a human premature aging disorder characterized by chromosomal instability. The disease is caused by the functional loss of WRN, a member of the RecQ-helicase family that plays an important role in DNA metabolic pathways. WRN contains four structurally folded domains comprising an exonuclease, a helicase, a winged-helix, and a helicase-and-ribonuclease D/C-terminal (HRDC) domain. In contrast to the accumulated knowledge pertaining to the biochemical functions of the three N-terminal domains, the function of C-terminal HRDC remains unknown. In this study, the crystal structure of the human WRN HRDC domain has been determined. The domain forms a bundle of alpha-helices similar to those of Saccharomyces cerevisiae Sgs1 and Escherichia coli RecQ. Surprisingly, the extra ten residues at each of the N and C termini of the domain were found to participate in the domain architecture by forming an extended portion of the first helix alpha1, and a novel looping motif that traverses straight along the domain surface, respectively. The motifs combine to increase the domain surface of WRN HRDC, which is larger than that of Sgs1 and E. coli.In WRN HRDC, neither of the proposed DNA-binding surfaces in Sgs1 or E. coli is conserved, and the domain was shown to lack DNA-binding ability in vitro. Moreover, the domain was shown to be thermostable and resistant to protease digestion, implying independent domain evolution in WRN. Coupled with the unique long linker region in WRN, the WRN HRDC may be adapted to play a distinct function in WRN that involves protein-protein interactions.
 
  Selected figure(s)  
 
Figure 2.
FIGURE 2. Crystal structure of the human WRN HRDC domain. A, front view (left) and top view (right) of WRN HRDC in a ribbon model. Secondary structure elements are labeled, and dimensions of the molecule are indicated. Molecular surface of the domain is shown in transparent gray (conventional HRDC core) and red (N- and C-terminal extensions unique to WRN). B, superimposition of WRN HRDC (green) with Sgs1 (19) (pink) and E. coli (20) (yellow) HRDCs. The orientation is the same as in A. The N and C termini of each molecule are labeled. Superimposition was performed using LSQMAN (56).
Figure 3.
FIGURE 3. C-terminal extended loop packed to the HRDC core. A,a stick model represents carbon atoms of the nine C-terminal residues (1227–1235, labeled with one-letter codes) shown in cyan, whereas the other part of the domain including N-terminal extended helix 1 is in green. The composite-omit density map (25) for the C-terminal residues is shown at the contour level of 1 . The orientation is similar to that in Fig. 2A (top view). B, schematic representation depicting the interactions between the C-terminal extended loop (cyan) and HRDC core, including helix 1(green). Hydrogen bonds are shown as dashed lines with distances (Å) shown. Two hydrophobic pockets on the HRDC core (pocket-1 formed by side chains from Thr^1152, Phe^1222, Cys^1223, and Asn^1226, and pocket-2 formed by Met^1190, Pro^1192, Asn^1197, Ile^1201, and Arg^1200) that are important for the binding of C-terminal residues are indicated.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 2717-2728) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20159459 K.A.Hoadley, and J.L.Keck (2010).
Werner helicase wings DNA binding.
  Structure, 18, 149-151.  
20159463 K.Kitano, S.Y.Kim, and T.Hakoshima (2010).
Structural basis for DNA strand separation by the unconventional winged-helix domain of RecQ helicase WRN.
  Structure, 18, 177-187.
PDB code: 3aaf
20639533 Y.M.Kim, and B.S.Choi (2010).
Structure and function of the regulatory HRDC domain from human Bloom syndrome protein.
  Nucleic Acids Res, 38, 7764-7777.
PDB code: 2kv2
19949442 A.Vindigni, and I.D.Hickson (2009).
RecQ helicases: multiple structures for multiple functions?
  HFSP J, 3, 153-164.  
19017267 M.P.Killoran, P.L.Kohler, J.P.Dillard, and J.L.Keck (2009).
RecQ DNA helicase HRDC domains are critical determinants in Neisseria gonorrhoeae pilin antigenic variation and DNA repair.
  Mol Microbiol, 71, 158-171.  
18702526 K.M.Sinha, N.C.Stephanou, M.C.Unciuleac, M.S.Glickman, and S.Shuman (2008).
Domain requirements for DNA unwinding by mycobacterial UvrD2, an essential DNA helicase.
  Biochemistry, 47, 9355-9364.  
18411208 M.P.Killoran, and J.L.Keck (2008).
Structure and function of the regulatory C-terminal HRDC domain from Deinococcus radiodurans RecQ.
  Nucleic Acids Res, 36, 3139-3149.
PDB code: 2rhf
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.