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PDBsum entry 1ruv

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Endoribonuclease PDB id
1ruv
Jmol
Contents
Protein chain
124 a.a. *
Ligands
UVC
TBU
Waters ×131
* Residue conservation analysis
PDB id:
1ruv
Name: Endoribonuclease
Title: Ribonuclease a-uridine vanadate complex: high resolution resolution x-ray structure (1.3 a)
Structure: Ribonuclease a. Chain: a. Ec: 3.1.27.5
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Resolution:
1.25Å     R-factor:   0.197    
Authors: J.E.Ladner,B.Wladkowski,L.A.Svensson,L.Sjolin,G.L.Gilliland
Key ref:
J.E.Ladner et al. (1997). X-ray structure of a ribonuclease A-uridine vanadate complex at 1.3 A resolution. Acta Crystallogr D Biol Crystallogr, 53, 290-301. PubMed id: 15299932 DOI: 10.1107/S090744499601582X
Date:
27-Jul-95     Release date:   01-Apr-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
124 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.5  - Pancreatic ribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     7 terms  

 

 
DOI no: 10.1107/S090744499601582X Acta Crystallogr D Biol Crystallogr 53:290-301 (1997)
PubMed id: 15299932  
 
 
X-ray structure of a ribonuclease A-uridine vanadate complex at 1.3 A resolution.
J.E.Ladner, B.D.Wladkowski, L.A.Svensson, L.Sjölin, G.L.Gilliland.
 
  ABSTRACT  
 
The X-ray crystal structure of a uridine vanadate-ribonuclease A complex has been determined at 1.3 A resolution. The resulting structure includes all 124 amino-acid residues, a uridine vanadate, 131 water molecules, and a single bound 2-methyl-2-propanol. Side chains of 11 surface residues showing discrete disorder were modeled with multiple conformations. The final crystallographic R factor is 0.197. Structures obtained from high-level ab initio quantum calculations of model anionic oxyvanadate compounds were used to probe the effects of starting structure on the refinement process and final structure of the penta-coordinate phosphorane analog, uridine vanadate. The least-squares refinement procedure gave rise to the same final structure of the inhibitor despite significantly different starting models. Comparison with the previously determined complex of ribonuclease A with uridine vanadate obtained from a joint X-ray/neutron analysis (6RSA) [Wlodawer, Miller & Sjölin (1983). Proc. Natl Acad. Sci. USA, 80, 3628-3631] reveals similarities in the overall enzyme structure and the relative position of the key active-site residues, Hisl2, His119 and Lys41, but significant differences in the V-O bond distances and angles. The influence of ligand binding on the enzyme structure is assessed by a comparison of the current X-ray structure with the phosphate-free ribonuclease A structure (7RSA) [Wlodawer, Svensson, Sjölin & Gilliland (1988). Biochemistry, 27, 2705-2717]. Ligand binding alters the solvent structure, distribution and number of residues with multiple conformations, and temperature factors of the protein atoms. In fact, the temperature factors of atoms of several residues that interact with the ligand are reduced, but those of the atoms of several residues remote from the active site exhibit marked increases.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. The active-site region of 1RUV. Hydrogen bonds be- tween selected atoms of the UV, the solvent and the pro- tein are indicated with dashed lines.
Figure 5.
Fig. 5. The UV in the active site of 1RUV with the associated basic residues, Hisl2, Lys41, and Hisll9. The geometry including bond angles and distances of the TBP is shown.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1997, 53, 290-301) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20124705 S.B.Larson, J.S.Day, C.Nguyen, R.Cudney, and A.McPherson (2010).
Structure of bovine pancreatic ribonuclease complexed with uridine 5'-monophosphate at 1.60 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 113-120.
PDB code: 3jw1
18274691 A.González Baró, I.Andersson, L.Pettersson, and A.Gorzsás (2008).
Speciation in the aqueous peroxovanadate-maltol and (peroxo)vanadate-uridine systems.
  Dalton Trans, (), 1095-1102.  
18508078 K.Kazakou, D.E.Holloway, S.H.Prior, V.Subramanian, and K.R.Acharya (2008).
Ribonuclease A homologues of the zebrafish: polymorphism, crystal structures of two representatives and their evolutionary implications.
  J Mol Biol, 380, 206-222.
PDB codes: 2vq8 2vq9
18808119 P.A.Sigala, D.A.Kraut, J.M.Caaveiro, B.Pybus, E.A.Ruben, D.Ringe, G.A.Petsko, and D.Herschlag (2008).
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.
  J Am Chem Soc, 130, 13696-13708.
PDB codes: 2inx 3cpo
17488874 A.T.Torelli, J.Krucinska, and J.E.Wedekind (2007).
A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization.
  RNA, 13, 1052-1070.
PDB codes: 2p7d 2p7e 2p7f
16301790 D.E.Holloway, G.B.Chavali, M.C.Hares, V.Subramanian, and K.R.Acharya (2005).
Structure of murine angiogenin: features of the substrate- and cell-binding regions and prospects for inhibitor-binding studies.
  Acta Crystallogr D Biol Crystallogr, 61, 1568-1578.
PDB codes: 2bwk 2bwl
14573867 D.D.Leonidas, G.B.Chavali, N.G.Oikonomakos, E.D.Chrysina, M.N.Kosmopoulou, M.Vlassi, C.Frankling, and K.R.Acharya (2003).
High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors.
  Protein Sci, 12, 2559-2574.
PDB codes: 1o0f 1o0h 1o0m 1o0n 1o0o
9636030 L.W.Schultz, D.J.Quirk, and R.T.Raines (1998).
His...Asp catalytic dyad of ribonuclease A: structure and function of the wild-type, D121N, and D121A enzymes.
  Biochemistry, 37, 8886-8898.
PDB codes: 3rsd 4rsd
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.