spacer
spacer

PDBsum entry 1ssb

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase(endoribonuclease) PDB id
1ssb
Jmol
Contents
Protein chains
113 a.a. *
11 a.a. *
Ligands
SO4
Waters ×95
* Residue conservation analysis
PDB id:
1ssb
Name: Hydrolase(endoribonuclease)
Title: A structural investigation of catalytically modified f12ol and f12oy semisynthetic ribonucleases
Structure: Ribonuclease a. Chain: a. Engineered: yes. Ribonuclease a. Chain: b. Engineered: yes
Source: Bos taurus. Bovine. Organism_taxid: 9913. Tissue: pancreas. Synthetic: yes
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.184    
Authors: V.S.J.Demel,M.S.Doscher,M.A.Glinn,P.D.Martin,M.L.Ram, B.F.P.Edwards
Key ref:
V.S.deMel et al. (1994). Structural investigation of catalytically modified F120L and F120Y semisynthetic ribonucleases. Protein Sci, 3, 39-50. PubMed id: 8142897 DOI: 10.1002/pro.5560030106
Date:
03-Aug-93     Release date:   30-Sep-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     6 terms  

 

 
DOI no: 10.1002/pro.5560030106 Protein Sci 3:39-50 (1994)
PubMed id: 8142897  
 
 
Structural investigation of catalytically modified F120L and F120Y semisynthetic ribonucleases.
V.S.deMel, M.S.Doscher, M.A.Glinn, P.D.Martin, M.L.Ram, B.F.Edwards.
 
  ABSTRACT  
 
The structures of two catalytically modified semisynthetic RNases obtained by replacing phenylalanine 120 with leucine and tyrosine have been determined and refined at a resolution of 2.0 A (R = 0.161 and 0.184, respectively). These structures have been compared with the refined 1.8-A structure (R = 0.204) of the fully active phenylalanine-containing enzyme (Martin PD, Doscher MS, Edwards BFP, 1987, J Biol Chem 262:15930-15938) and with the catalytically defective D121A (2.0 A, R = 0.172) and D121N (2.0 A, R = 0.186) analogs (deMel VSJ, Martin PD, Doscher MS, Edwards BFP, 1992, J Biol Chem 267:247-256). The movement away from the active site of the loop containing residues 65-72 is seen in all three catalytically defective analogs--F120L, D121A, and D121N--but not in the fully active (or hyperactive) F120Y. The insertion of the phenolic hydroxyl of Tyr 120 into a hydrogen-bonding network involving the hydroxyl group of Ser 123 and a water molecule in F120Y is the likely basis for the hyperactivity toward uridine 2',3'-cyclic phosphate previously found for this analog (Hodges RS, Merrifield RB, 1974, Int J Pept Protein Res 6:397-405) as well as the threefold increase in KM for cytidine 2',3'-cyclic phosphate found for this analog by ourselves.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Preparation and assemblyofRNase 1-118:111-124. Th schematic diagram shows thepreparation ofRNase -1 18 by limited proteolytic digestion nd its ssem- blywith a chemically synthesized 11 1-124 tetradecapeptide into a noncovalent com- plex (which is fully active when no amino acid replacements have been made).
Figure 10.
Fig. 10. Hypothetical hydrogen-bonding interaction between Ser 123 and the pyrimidine ring of uracil- or cytosine-containing ubstratess proposed by Hodges and Merrifield (1975:Fig. 1). n the Hodges- Merrifield model, Ser123 interacts directly with the base, requiring that it function asa donor with uracil andas an acceptor with cytosine. The 4.87-A distance between Ser 123 OG and the uracil 04 in the RNase Ahridine vanadate structure (Borah et al., 1985; Protein Data Bankfile 6RSA) reveals that a direct hydrogen bond is notpossible. In our model (see Fig. 9), an intervening water molecule functions asa donor or ac- ceptor depending upon which base is presented, while Ser 123 always hydrogen bonds to this water asan acceptor whether the base is or cytosine.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1994, 3, 39-50) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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.

 

spacer

spacer