spacer
spacer

PDBsum entry 2w5m

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2w5m
Jmol
Contents
Protein chains
124 a.a. *
Ligands
POP ×2
Waters ×125
* Residue conservation analysis
PDB id:
2w5m
Name: Hydrolase
Title: Rnase a-pyrophosphate ion complex
Structure: Ribonuclease pancreatic. Chain: a, b. Synonym: rnase 1, rnase a, ribonuclease a. Ec: 3.1.27.5
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas. Other_details: sigma chemical co.
Resolution:
1.80Å     R-factor:   0.187     R-free:   0.222
Authors: G.B.Chavali,D.E.Holloway,M.D.Baker,K.R.Acharya
Key ref: D.E.Holloway et al. (2009). Influence of naturally-occurring 5'-pyrophosphate-linked substituents on the binding of adenylic inhibitors to ribonuclease a: an X-ray crystallographic study. Biopolymers, 91, 995. PubMed id: 19191310
Date:
10-Dec-08     Release date:   17-Feb-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
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  

 

 
Biopolymers 91:995 (2009)
PubMed id: 19191310  
 
 
Influence of naturally-occurring 5'-pyrophosphate-linked substituents on the binding of adenylic inhibitors to ribonuclease a: an X-ray crystallographic study.
D.E.Holloway, G.B.Chavali, D.D.Leonidas, M.D.Baker, K.R.Acharya.
 
  ABSTRACT  
 
Ribonuclease A is the archetype of a functionally diverse superfamily of vertebrate-specific ribonucleases. Inhibitors of its action have potential use in the elucidation of the in vivo roles of these enzymes and in the treatment of pathologies associated therewith. Derivatives of adenosine 5'-pyrophosphate are the most potent nucleotide-based inhibitors known. Here, we use X-ray crystallography to visualize the binding of four naturally-occurring derivatives that contain 5'-pyrophosphate-linked extensions. 5'-ATP binds with the adenine occupying the B(2) subsite in the manner of an RNA substrate but with the gamma-phosphate at the P(1) subsite. Diadenosine triphosphate (Ap(3)A) binds with the adenine in syn conformation, the beta-phosphate as the principal P(1) subsite ligand and without order beyond the gamma-phosphate. NADPH and NADP(+) bind with the adenine stacked against an alternative rotamer of His119, the 2'-phosphate at the P(1) subsite, and without order beyond the 5'-alpha-phosphate. We also present the structure of the complex formed with pyrophosphate ion. The structural data enable existing kinetic data on the binding of these compounds to a variety of ribonucleases to be rationalized and suggest that as the complexity of the 5'-linked extension increases, the need to avoid unfavorable contacts places limitations on the number of possible binding modes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21205197 N.Thiyagarajan, B.D.Smith, R.T.Raines, and K.R.Acharya (2011).
Functional and structural analyses of N-acylsulfonamide-linked dinucleoside inhibitors of RNase A.
  FEBS J, 278, 541-549.
PDB codes: 2xog 2xoi
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.