spacer
spacer

PDBsum entry 4srn

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase(nucleic acid,RNA) PDB id
4srn
Jmol
Contents
Protein chains
113 a.a. *
11 a.a. *
Ligands
SO4
Waters ×111
* Residue conservation analysis
PDB id:
4srn
Name: Hydrolase(nucleic acid,RNA)
Title: Structural changes that accompany the reduced catalytic effi two semisynthetic ribonuclease analogs
Structure: Ribonuclease a. Chain: a. Engineered: yes. Ribonuclease a. Chain: b. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organism_taxid: 9913
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.172    
Authors: V.S.J.Demel,P.D.Martin,M.S.Doscher,B.F.P.Edwards
Key ref: V.S.deMel et al. (1992). Structural changes that accompany the reduced catalytic efficiency of two semisynthetic ribonuclease analogs. J Biol Chem, 267, 247-256. PubMed id: 1730593
Date:
20-May-91     Release date:   20-Dec-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
11 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B: 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  

 

 
J Biol Chem 267:247-256 (1992)
PubMed id: 1730593  
 
 
Structural changes that accompany the reduced catalytic efficiency of two semisynthetic ribonuclease analogs.
V.S.deMel, P.D.Martin, M.S.Doscher, B.F.Edwards.
 
  ABSTRACT  
 
The structures of two catalytically defective semi-synthetic RNases obtained by replacing aspartic acid 121 with asparagine or alanine have been determined and refined at a resolution of 2.0 A (R = 0.186 and 0.172, respectively). When these structures are compared with the refined 1.8-A structure (R = 0.204) of the fully active aspartic acid-containing enzyme (Martin, P.D., Doscher, M.S., and Edwards, B. F. P. (1987) J. Biol. Chem. 262, 15930-15938), numerous and widespread changes, much greater in number and magnitude than the small structural variations noted previously between the semisynthetic complex and RNase A, are found to have occurred. These changes include the movement of the loop containing residues 65-72 away from the active site, a more or less generalized relocation of crystallographically bound water molecules, and a number of rearrangements in the hydrogen bonding network at the active site. Most changes are far removed from the immediate site of the modifications and are distributed essentially throughout the molecule. The details of many of these changes are unique to each analog. In the asparagine analog, a destabilization in the positioning of active site residue His-119 also appears to have occurred.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
16335788 D.Gaur, and J.K.Batra (2005).
Role of aspartic acid 121 in human pancreatic ribonuclease catalysis.
  Mol Cell Biochem, 275, 95.  
11742124 E.Chatani, R.Hayashi, H.Moriyama, and T.Ueki (2002).
Conformational strictness required for maximum activity and stability of bovine pancreatic ribonuclease A as revealed by crystallographic study of three Phe120 mutants at 1.4 A resolution.
  Protein Sci, 11, 72-81.
PDB codes: 1eic 1eid 1eie 1fs3
11876642 G.J.Swaminathan, D.E.Holloway, K.Veluraja, and K.R.Acharya (2002).
Atomic resolution (0.98 A) structure of eosinophil-derived neurotoxin.
  Biochemistry, 41, 3341-3352.
PDB code: 1gqv
10049337 D.J.Quirk, and R.T.Raines (1999).
His ... Asp catalytic dyad of ribonuclease A: histidine pKa values in the wild-type, D121N, and D121A enzymes.
  Biophys J, 76, 1571-1579.  
9649305 J.Hofsteenge, C.Moldow, A.M.Vicentini, O.Zelenko, Z.Jarai-Kote, and U.Neumann (1998).
A single amino acid substitution changes ribonuclease 4 from a uridine-specific to a cytidine-specific enzyme.
  Biochemistry, 37, 9250-9257.  
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
9578571 R.Shapiro (1998).
Structural features that determine the enzymatic potency and specificity of human angiogenin: threonine-80 and residues 58-70 and 116-123.
  Biochemistry, 37, 6847-6856.  
  9385633 A.C.Wallace, N.Borkakoti, and J.M.Thornton (1997).
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.
  Protein Sci, 6, 2308-2323.  
8973167 A.A.Fedorov, D.Joseph-McCarthy, E.Fedorov, D.Sirakova, I.Graf, and S.C.Almo (1996).
Ionic interactions in crystalline bovine pancreatic ribonuclease A.
  Biochemistry, 35, 15962-15979.
PDB codes: 1rno 1rnq 1rnw 1rnx 1rny 1rnz
  7756988 I.Zegers, D.Maes, M.H.Dao-Thi, F.Poortmans, R.Palmer, and L.Wyns (1994).
The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules.
  Protein Sci, 3, 2322-2339.
PDB codes: 1rpf 1rpg 1rph
8159679 K.R.Acharya, R.Shapiro, S.C.Allen, J.F.Riordan, and B.L.Vallee (1994).
Crystal structure of human angiogenin reveals the structural basis for its functional divergence from ribonuclease.
  Proc Natl Acad Sci U S A, 91, 2915-2919.
PDB code: 1ang
8159680 N.Russo, R.Shapiro, K.R.Acharya, J.F.Riordan, and B.L.Vallee (1994).
Role of glutamine-117 in the ribonucleolytic activity of human angiogenin.
  Proc Natl Acad Sci U S A, 91, 2920-2924.  
7919003 T.D.Veenstra, and L.Lee (1994).
NMR study of the positions of His-12 and His-119 in the ribonuclease A-uridine vanadate complex.
  Biophys J, 67, 331-335.  
  8142897 V.S.deMel, M.S.Doscher, M.A.Glinn, P.D.Martin, M.L.Ram, and B.F.Edwards (1994).
Structural investigation of catalytically modified F120L and F120Y semisynthetic ribonucleases.
  Protein Sci, 3, 39-50.
PDB codes: 1ssa 1ssb
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.