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PDBsum entry 2qca

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protein ligands links
Hydrolase PDB id
2qca
Jmol
Contents
Protein chain
124 a.a. *
Ligands
DGP ×2
Waters ×137
* Residue conservation analysis
PDB id:
2qca
Name: Hydrolase
Title: A new crystal form of bovine pancreatic rnase a in complex w deoxyguanosine-5'-monophosphate
Structure: Ribonuclease pancreatic. Chain: a. Synonym: rnase 1, rnase a. Ec: 3.1.27.5
Source: Bos taurus. Cattle. Organism_taxid: 9913. Tissue: pancreas
Resolution:
1.33Å     R-factor:   0.125     R-free:   0.177
Authors: S.B.Larson,J.S.Day,R.Cudney,A.Mcpherson,Center For High-Thro Structural Biology (Chtsb)
Key ref:
S.B.Larson et al. (2007). A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate. Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 728-733. PubMed id: 17768339 DOI: 10.1107/S1744309107039565
Date:
19-Jun-07     Release date:   03-Jul-07    
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/S1744309107039565 Acta Crystallogr Sect F Struct Biol Cryst Commun 63:728-733 (2007)
PubMed id: 17768339  
 
 
A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate.
S.B.Larson, J.S.Day, R.Cudney, A.McPherson.
 
  ABSTRACT  
 
The structure of bovine pancreatic RNase A has been determined in complex with 2'-deoxyguanosine-5'-monophosphate (dGMP) at 1.33 A resolution at room temperature in a previously unreported unit cell belonging to space group P3(1). There are two molecules of nucleotide per enzyme molecule, one of which lies in the active-site cleft in the productive binding mode, whilst the guanine base of the other dGMP occupies the pyrimidine-specific binding site in a nonproductive mode such that it forms hydrogen bonds to the phosphate group of the first dGMP. This is the first RNase A structure containing a guanine base in the B2 binding site. Each dGMP molecule is involved in intermolecular interactions with adjacent RNase A molecules in the lattice and the two nucleotides appear to direct the formation of the crystal lattice. Because GMP may be produced during degradation of RNA, this association could represent an inhibitor complex and thereby affect the observed enzyme kinetics.
 
  Selected figure(s)  
 
Figure 2.
(a) Detailed hydrogen-bonding interactions of dGMP200 with two molecules of RNase A, as well as with dGMP300. (b) The corresponding interactions of dGMP300. The ring-to-ring separation is approximately 3.5 A between the guanine ring and Tyr115. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 September 1; 63(Pt 9): 728–733. Published online 2007 August 31. doi: 10.1107/S1744309107039565. Copyright [copyright] International Union of Crystallography 2007
Figure 4.
Relative positions of the purine rings in (a) structure 1rcn, (b) the present structure and (c) structure 1z6d after superposition of the C^[alpha] atoms of the active-site residues His12, Thr45, His119 and Phe120. The active-site residues in the background are displayed as line drawings to establish a point of reference for the positioning of the purine rings in each structure. The interactions for each purine ring are indicated by dashed lines. Residue Asn71 is fairly constantly disposed with respect to the active-site residues, while Gln69 and Glu111 move to accommodate the various base rings of the bound nucleotides at the B2 site. The displacement is approximately in the plane of the adenine ring with a magnitude of [similar]2 A for the guanine ring and of [similar]4 A for the hypoxanthine ring. This demonstrates how the enzyme can accommodate a variety of bases in the B2 site. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 September 1; 63(Pt 9): 728–733. Published online 2007 August 31. doi: 10.1107/S1744309107039565. Copyright [copyright] International Union of Crystallography 2007
 
  The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallogr Sect F Struct Biol Cryst Commun (2007, 63, 728-733) copyright 2007.  
  Figures were selected by an automated process.