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PDBsum entry 1tqm
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Ribosome PDB id
1tqm

 

 

 

 

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JSmol PyMol  
Contents
Protein chain
269 a.a. *
Ligands
ANP
Waters ×197
* Residue conservation analysis
PDB id:
1tqm
Name: Ribosome
Title: Crystal structure of a. Fulgidus rio2 serine protein kinase bound to amppnp
Structure: Conserved hypothetical protein. Chain: a. Synonym: rio2. Engineered: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 224325. Strain: dsm 4304. Gene: rio2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.99Å     R-factor:   0.174     R-free:   0.228
Authors: N.Laronde-Leblanc,A.Wlodawer
Key ref:
N.LaRonde-LeBlanc and A.Wlodawer (2004). Crystal structure of A. fulgidus Rio2 defines a new family of serine protein kinases. Structure, 12, 1585-1594. PubMed id: 15341724 DOI: 10.1016/j.str.2004.06.016
Date:
17-Jun-04     Release date:   28-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O30245  (RIO2_ARCFU) -  RIO-type serine/threonine-protein kinase Rio2 from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
Seq:
Struc: 		282 a.a.
269 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.11.1  - non-specific serine/threonine protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H+
2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H+
L-seryl-[protein]
 + ATP
 = O-phospho-L-seryl-[protein]
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity 		+ ADP
 + H(+)
L-threonyl-[protein]
 + ATP
 = O-phospho-L-threonyl-[protein]
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity 		+ ADP
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2004.06.016 Structure 12:1585-1594 (2004)
PubMed id: 15341724  
 
 
Crystal structure of A. fulgidus Rio2 defines a new family of serine protein kinases.
N.LaRonde-LeBlanc, A.Wlodawer.
 
  ABSTRACT  
 
The RIO family of atypical serine/threonine kinases contains two subfamilies, Rio1 and Rio2, highly conserved from archaea to man. Both RIO proteins from Saccharomyces cerevisiae catalyze serine phosphorylation in vitro, and the presence of conserved catalytic residues is required for cell viability. The activity of Rio2 is necessary for rRNA cleavage in 40S ribosomal subunit maturation. We solved the X-ray crystal structure of Archaeoglobus fulgidus Rio2, with and without bound nucleotides, at 2.0 A resolution. The C-terminal RIO domain is indeed structurally homologous to protein kinases, although it differs from known serine kinases in ATP binding and lacks the regions important for substrate binding. Unexpectedly, the N-terminal Rio2-specific domain contains a winged helix fold, seen primarily in DNA-binding proteins. These discoveries have implications in determining the target and function of RIO proteins and define a distinct new family of protein kinases.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Overall Structure of Rio2The crystal structure of AfRio2 shows a bilobal kinase domain (orange and red) tightly connected to an N-terminal winged helix domain (blue). The green "hinge" region connects the N- and C-terminal lobes of the kinase domain. The bound ATP analog, AMPPNP, is shown in a ball-and-stick representation. This figure was made using Ribbons (Carson, 1991).
 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 1585-1594) copyright 2004.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23104056 S.Ferreira-Cerca, V.Sagar, T.Schäfer, M.Diop, A.M.Wesseling, H.Lu, E.Chai, E.Hurt, and N.Laronde-Leblanc (2012).
ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit.
  Nat Struct Mol Biol, 19, 1316-1323.
PDB codes: 4gyg 4gyi
20118261 B.Wang, S.Yang, L.Zhang, and Z.G.He (2010).
Archaeal eukaryote-like serine/threonine protein kinase interacts with and phosphorylates a forkhead-associated-domain-containing protein.
  J Bacteriol, 192, 1956-1964.  
19850913 B.S.Strunk, and K.Karbstein (2009).
Powering through ribosome assembly.
  RNA, 15, 2083-2104.  
19274099 M.Aivaliotis, B.Macek, F.Gnad, P.Reichelt, M.Mann, and D.Oesterhelt (2009).
Ser/Thr/Tyr protein phosphorylation in the archaeon Halobacterium salinarum--a representative of the third domain of life.
  PLoS ONE, 4, e4777.  
19050074 A.C.Kimmelman, A.F.Hezel, A.J.Aguirre, H.Zheng, J.H.Paik, H.Ying, G.C.Chu, J.X.Zhang, E.Sahin, G.Yeo, A.Ponugoti, R.Nabioullin, S.Deroo, S.Yang, X.Wang, J.P.McGrath, M.Protopopova, E.Ivanova, J.Zhang, B.Feng, M.S.Tsao, M.Redston, A.Protopopov, Y.Xiao, P.A.Futreal, W.C.Hahn, D.S.Klimstra, L.Chin, and R.A.DePinho (2008).
Genomic alterations link Rho family of GTPases to the highly invasive phenotype of pancreas cancer.
  Proc Natl Acad Sci U S A, 105, 19372-19377.  
18808669 M.Hu, N.Laronde-Leblanc, P.W.Sternberg, and R.B.Gasser (2008).
Tv-RIO1 - an atypical protein kinase from the parasitic nematode Trichostrongylus vitrinus.
  Parasit Vectors, 1, 34.  
  18259057 P.Bahti, S.Chen, Y.Li, N.Shaw, X.Zhang, M.Zhang, C.Cheng, G.Song, J.Yin, H.Zhang, D.Che, A.Abbas, H.Xu, B.C.Wang, and Z.J.Liu (2008).
Purification, crystallization and preliminary crystallographic analysis of the non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 91-93.  
17557329 D.Miranda-Saavedra, and G.J.Barton (2007).
Classification and functional annotation of eukaryotic protein kinases.
  Proteins, 68, 893-914.  
17912359 J.D.Knight, B.Qian, D.Baker, and R.Kothary (2007).
Conservation, variability and the modeling of active protein kinases.
  PLoS ONE, 2, e982.  
17355172 N.Kannan, S.S.Taylor, Y.Zhai, J.C.Venter, and G.Manning (2007).
Structural and functional diversity of the microbial kinome.
  PLoS Biol, 5, e17.  
17961230 S.Y.Ku, K.A.Cornell, and P.L.Howell (2007).
Structure of Arabidopsis thaliana 5-methylthioribose kinase reveals a more occluded active site than its bacterial homolog.
  BMC Struct Biol, 7, 70.
PDB code: 2pyw
15808743 L.Aravind, V.Anantharaman, S.Balaji, M.M.Babu, and L.M.Iyer (2005).
The many faces of the helix-turn-helix domain: transcription regulation and beyond.
  FEMS Microbiol Rev, 29, 231-262.  
16164760 M.Parsons, E.A.Worthey, P.N.Ward, and J.C.Mottram (2005).
Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi.
  BMC Genomics, 6, 127.  
16183636 N.LaRonde-LeBlanc, and A.Wlodawer (2005).
A family portrait of the RIO kinases.
  J Biol Chem, 280, 37297-37300.  
15943813 N.LaRonde-LeBlanc, T.Guszczynski, T.Copeland, and A.Wlodawer (2005).
Autophosphorylation of Archaeoglobus fulgidus Rio2 and crystal structures of its nucleotide-metal ion complexes.
  FEBS J, 272, 2800-2810.
PDB codes: 1zao 1zar
15983420 Z.Dauter, I.Botos, N.LaRonde-LeBlanc, and A.Wlodawer (2005).
Pathological crystallography: case studies of several unusual macromolecular crystals.
  Acta Crystallogr D Biol Crystallogr, 61, 967-975.
PDB codes: 1z0t 1z0v
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.

 

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