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PDBsum entry 1o4w

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protein links
Translation PDB id
1o4w
Jmol
Contents
Protein chain
125 a.a. *
Waters ×90
* Residue conservation analysis
PDB id:
1o4w
Name: Translation
Title: Crystal structure of a pin (pilt n-terminus) domain containi (af0591) from archaeoglobus fulgidus at 1.90 a resolution
Structure: Pin (pilt n-terminus) domain. Chain: a. Engineered: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 2234. Gene: af0591. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
1.90Å     R-factor:   0.191     R-free:   0.235
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
I.Levin et al. (2004). Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution. Proteins, 56, 404-408. PubMed id: 15211526 DOI: 10.1002/prot.20090
Date:
16-Jul-03     Release date:   29-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O29664  (VAPC9_ARCFU) -  Ribonuclease VapC9
Seq:
Struc:
135 a.a.
125 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     small-subunit processome   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1002/prot.20090 Proteins 56:404-408 (2004)
PubMed id: 15211526  
 
 
Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution.
I.Levin, R.Schwarzenbacher, R.Page, P.Abdubek, E.Ambing, T.Biorac, L.S.Brinen, J.Campbell, J.M.Canaves, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, E.Hampton, L.Jaroszewski, C.Karlak, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, S.A.Lesley, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, K.Quijano, R.Reyes, F.Rezezadeh, A.Robb, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, F.von Delft, X.Wang, B.West, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, I.A.Wilson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal structure of AF0591. (A) Ribbon diagram of Archaeoglobus fulgidus AF0591 color coded from N-terminus (blue) to C-terminus (red) showing the domain organization. The disulfide-bond between Cys13 and Cys100 is shown in ball and stick (orange). -Helices H1-H6, and -strands ( 1- 5) in -sheet A are indicated. (B) Diagram showing the secondary structure elements in AF0591 superimposed on its primary sequence. The disulfide-bond (Cys13-Cys100) is indicated, and the disordered regions are depicted by a dashed line with the corresponding sequence in brackets. Strands are labeled according to their -sheet (A). The location of -turns are also indicated. Mse refers to seleno-methionine.
Figure 2.
Figure 2. (A) Ribbon diagram of the AF0591 dimer. (B) Ribbon diagram of a superposition of AF0591 (rainbow) and the catalytic domain (residues 1-174) of 5 -3 exonuclease from Bacteriophage T5 (gray). -Helices and -strands are indicated for AF0591. (C) Close-up view of the active site. Active site residues as observed in T5 5 -3 exonuclease (labels shown in brackets) and their counterparts in AF0591 are shown in ball and stick. Colors are the same as in (B). The side-chain of E108 in AF0591 was disordered and, therefore, not modeled.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 56, 404-408) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19706509 A.C.Lamanna, and K.Karbstein (2009).
Nob1 binds the single-stranded cleavage site D at the 3'-end of 18S rRNA with its PIN domain.
  Proc Natl Acad Sci U S A, 106, 14259-14264.  
19060898 D.Schaeffer, B.Tsanova, A.Barbas, F.P.Reis, E.G.Dastidar, M.Sanchez-Rotunno, C.M.Arraiano, and A.van Hoof (2009).
The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities.
  Nat Struct Mol Biol, 16, 56-62.  
18398909 R.D.Bunker, J.L.McKenzie, E.N.Baker, and V.L.Arcus (2008).
Crystal structure of PAE0151 from Pyrobaculum aerophilum, a PIN-domain (VapC) protein from a toxin-antitoxin operon.
  Proteins, 72, 510-518.
PDB code: 2fe1
17557331 D.Takeshita, S.Zenno, W.C.Lee, K.Saigo, and M.Tanokura (2007).
Crystal structure of the PIN domain of human telomerase-associated protein EST1A.
  Proteins, 68, 980-989.
PDB code: 2dok
17355871 K.A.Satyshur, G.A.Worzalla, L.S.Meyer, E.K.Heiniger, K.G.Aukema, A.M.Misic, and K.T.Forest (2007).
Crystal structures of the pilus retraction motor PilT suggest large domain movements and subunit cooperation drive motility.
  Structure, 15, 363-376.
PDB codes: 2ewv 2eww 2eyu 2gsz
17053788 F.Glavan, I.Behm-Ansmant, E.Izaurralde, and E.Conti (2006).
Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex.
  EMBO J, 25, 5117-5125.
PDB codes: 2hww 2hwx 2hwy
  16511228 B.Collins, R.C.Stevens, and R.Page (2005).
Crystallization Optimum Solubility Screening: using crystallization results to identify the optimal buffer for protein crystal formation.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 1035-1038.  
  16511069 J.Jeyakanthan, E.Inagaki, C.Kuroishi, and T.H.Tahirov (2005).
Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 463-468.
PDB codes: 1v96 1ye5
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.