PDBsum entry 1yt3

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Hydrolase,translation PDB id
Protein chain
375 a.a. *
SO4 ×7
_ZN ×5
Waters ×492
* Residue conservation analysis
PDB id:
Name: Hydrolase,translation
Title: Crystal structure of escherichia coli rnase d, an exoribonuclease involved in structured RNA processing
Structure: Ribonuclease d. Chain: a. Synonym: rnase d. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: rnd. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.60Å     R-factor:   0.196     R-free:   0.216
Authors: Y.Zuo,Y.Wang,A.Malhotra
Key ref:
Y.Zuo et al. (2005). Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing. Structure, 13, 973-984. PubMed id: 16004870 DOI: 10.1016/j.str.2005.04.015
09-Feb-05     Release date:   09-Aug-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P09155  (RND_ECOLI) -  Ribonuclease D
375 a.a.
375 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Ribonuclease D.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Cofactor: Mg(2+) or cobalt cation or Mn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   2 terms 
  Biological process     nucleic acid phosphodiester bond hydrolysis   7 terms 
  Biochemical function     catalytic activity     9 terms  


DOI no: 10.1016/j.str.2005.04.015 Structure 13:973-984 (2005)
PubMed id: 16004870  
Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing.
Y.Zuo, Y.Wang, A.Malhotra.
RNase D (RND) is one of seven exoribonucleases identified in Escherichia coli. RNase D has homologs in many eubacteria and eukaryotes, and has been shown to contribute to the 3' maturation of several stable RNAs. Here, we report the 1.6 A resolution crystal structure of E. coli RNase D. The conserved DEDD residues of RNase D fold into an arrangement very similar to the Klenow fragment exonuclease domain. Besides the catalytic domain, RNase D also contains two structurally similar alpha-helical domains with no discernible sequence homology between them. These closely resemble the HRDC domain previously seen in RecQ-family helicases and several other proteins acting on nucleic acids. More interestingly, the DEDD catalytic domain and the two helical domains come together to form a ring-shaped structure. The ring-shaped architecture of E. coli RNase D and the HRDC domains likely play a major role in determining the substrate specificity of this exoribonuclease.
  Selected figure(s)  
Figure 1.
Figure 1. Multiple Alignment of RNase D-Related Sequences
Sequences are from the NCBI nonredundant protein sequence database. Sequence included here are: RND_ECOLI, E. coli RNase D (accession no. G133152); RND_MYCTU, M. tuberculosis Rv2681 protein, a putative RNase D (G15609818); RND_AGRTU, putative A. tumefaciens RNase D (G13195121); RRP6_YEAST, S. cerevisiae RRP6 protein, an exosome component (G14195186); PMC2_HUMAN, the human RRP6 equivalent (G8928564); RND_RICPR, putative R. prowazekii RNase D (G7467941); RND_SYNY3, putative Synechocystis RNase D (G1001530); and RND2_AGRTU, another A. tumefaciens RNase D-related protein (G17937803). These sequences are chosen because they are representative: RRP6_YEAST and PMC2_HUMAN are eukaryotic RNase D homologs; RND_MYCTU and RND_AGRTU are two distant bacterial homologs of E. coli RNase D; the other three sequences are distantly related to E. coli RNase D, but lacking one (RND_RICPR) or both (RND_SYNY3 and RND2_AGRTU) C-terminal domains. This sequence alignment was initially generated by ClustalX and manually adjusted based on secondary structure predictions due to very weak sequence conservation, especially at the C-terminal domain. Many other related sequences (not shown) have been used to help produce this sequence alignment. The conserved DEDDy residues are marked with red triangles, and are distributed among three exo motifs (Zuo and Deutscher, 2001). Residues conserved among most RNase D homologs are boxed and colored. Highly conserved residues are highlighted in red. The numbering on the top is according to E. coli RNase D sequence.
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 973-984) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
21317904 Y.Y.Hsiao, C.C.Yang, C.L.Lin, J.L.Lin, Y.Duh, and H.S.Yuan (2011).
Structural basis for RNA trimming by RNase T in stable RNA 3'-end maturation.
  Nat Chem Biol, 7, 236-243.
PDB codes: 3ngy 3ngz 3nh0 3nh1 3nh2
20301164 R.Tomecki, K.Drazkowska, and A.Dziembowski (2010).
Mechanisms of RNA degradation by the eukaryotic exosome.
  Chembiochem, 11, 938-945.  
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
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.  
19042972 S.G.Ozanick, X.Wang, M.Costanzo, R.L.Brost, C.Boone, and J.T.Anderson (2009).
Rex1p deficiency leads to accumulation of precursor initiator tRNAMet and polyadenylation of substrate RNAs in Saccharomyces cerevisiae.
  Nucleic Acids Res, 37, 298-308.  
18940861 K.P.Callahan, and J.S.Butler (2008).
Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p.
  Nucleic Acids Res, 36, 6645-6655.  
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
18658245 Z.Bukowy, J.A.Harrigan, D.A.Ramsden, B.Tudek, V.A.Bohr, and T.Stevnsner (2008).
WRN Exonuclease activity is blocked by specific oxidatively induced base lesions positioned in either DNA strand.
  Nucleic Acids Res, 36, 4975-4987.  
17189683 J.A.Worrall, and B.F.Luisi (2007).
Information available at cut rates: structure and mechanism of ribonucleases.
  Curr Opin Struct Biol, 17, 128-137.  
17229737 J.M.Choi, S.Y.Kang, W.J.Bae, K.S.Jin, M.Ree, and Y.Cho (2007).
Probing the roles of active site residues in the 3'-5' exonuclease of the Werner syndrome protein.
  J Biol Chem, 282, 9941-9951.  
17148451 K.Kitano, N.Yoshihara, and T.Hakoshima (2007).
Crystal structure of the HRDC domain of human Werner syndrome protein, WRN.
  J Biol Chem, 282, 2717-2728.
PDB codes: 2e1e 2e1f
17437714 Y.Zuo, H.Zheng, Y.Wang, M.Chruszcz, M.Cymborowski, T.Skarina, A.Savchenko, A.Malhotra, and W.Minor (2007).
Crystal structure of RNase T, an exoribonuclease involved in tRNA maturation and end turnover.
  Structure, 15, 417-428.
PDB codes: 2f96 2is3
16955096 D.Grossman, and A.van Hoof (2006).
RNase II structure completes group portrait of 3' exoribonucleases.
  Nat Struct Mol Biol, 13, 760-761.  
16281054 M.Wu, M.Reuter, H.Lilie, Y.Liu, E.Wahle, and H.Song (2005).
Structural insight into poly(A) binding and catalytic mechanism of human PARN.
  EMBO J, 24, 4082-4093.
PDB codes: 2a1r 2a1s
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 codes are shown on the right.