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PDBsum entry 3rsk

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Hydrolase PDB id
3rsk
Jmol
Contents
Protein chain
124 a.a. *
Ligands
ACT
Waters ×82
* Residue conservation analysis
PDB id:
3rsk
Name: Hydrolase
Title: Structure of the k7a/r10a/k66a variant of ribonuclease a
Structure: Ribonuclease a. Chain: a. Engineered: yes. Mutation: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Cell_line: bl21. Organ: pancreas. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.174    
Authors: L.W.Schultz,B.M.Fisher,R.T.Raines
Key ref:
L.W.Schultz et al. (1998). His...Asp catalytic dyad of ribonuclease A: structure and function of the wild-type, D121N, and D121A enzymes. Biochemistry, 37, 8886-8898. PubMed id: 9636030 DOI: 10.1021/bi972766q
Date:
09-Apr-98     Release date:   15-Jul-98    
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
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 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: 10.1021/bi972766q Biochemistry 37:8886-8898 (1998)
PubMed id: 9636030  
 
 
His...Asp catalytic dyad of ribonuclease A: structure and function of the wild-type, D121N, and D121A enzymes.
L.W.Schultz, D.J.Quirk, R.T.Raines.
 
  ABSTRACT  
 
The side chains of histidine and aspartate residues form a hydrogen bond in the active sites of many enzymes. In serine proteases, the His...Asp hydrogen bond of the catalytic triad is known to contribute greatly to catalysis, perhaps via the formation of a low-barrier hydrogen bond. In bovine pancreatic ribonuclease A (RNase A), the His...Asp dyad is composed of His119 and Asp121. Previously, site-directed mutagenesis was used to show that His119 has a fundamental role, to act as an acid during catalysis of RNA cleavage [Thompson, J. E., and Raines, R. T. (1994) J. Am. Chem. Soc. 116, 5467-5468]. Here, Asp121 was replaced with an asparagine or alanine residue. The crystalline structures of the two variants were determined by X-ray diffraction analysis to a resolution of 1.6 A with an R-factor of 0.18. Replacing Asp121 with an asparagine or alanine residue does not perturb the overall conformation of the enzyme. In the structure of D121N RNase A, Ndelta rather than Odelta of Asn121 faces His119. This alignment in the crystalline state is unlikely to exist in solution because catalysis by the D121N variant is not compromised severely. The steady-state kinetic parameters for catalysis by the wild-type and variant enzymes were determined for the cleavage of uridylyl(3'-->5')adenosine and poly(cytidylic acid), and for the hydrolysis of uridine 2',3'-cyclic phosphate. Replacing Asp121 decreases the values of kcat/Km and kcat for cleavage by 10-fold (D121N) and 10(2)-fold (D121A). Replacing Asp121 also decreases the values of kcat/Km and kcat for hydrolysis by 10(0. 5)-fold (D121N) and 10-fold (D121A) but has no other effect on the pH-rate profiles for hydrolysis. There is no evidence for the formation of a low-barrier hydrogen bond between His119 and either an aspartate or an asparagine residue at position 121. Apparently, the major role of Asp121 is to orient the proper tautomer of His119 for catalysis. Thus, the mere presence of a His...Asp dyad in an enzymic active site is not a mandate for its being crucial in effecting catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21050179 E.Pizzo, A.Merlino, M.Turano, I.Russo Krauss, F.Coscia, A.Zanfardino, M.Varcamonti, A.Furia, C.Giancola, L.Mazzarella, F.Sica, and G.D'Alessio (2010).
A new RNase sheds light on the RNase/angiogenin subfamily from zebrafish.
  Biochem J, 433, 345-355.
PDB codes: 3ljd 3lje 3ln8
18502788 A.S.Patana, M.Kurkela, M.Finel, and A.Goldman (2008).
Mutation analysis in UGT1A9 suggests a relationship between substrate and catalytic residues in UDP-glucuronosyltransferases.
  Protein Eng Des Sel, 21, 537-543.  
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
17615241 E.D.Watt, H.Shimada, E.L.Kovrigin, and J.P.Loria (2007).
The mechanism of rate-limiting motions in enzyme function.
  Proc Natl Acad Sci U S A, 104, 11981-11986.  
16730994 D.D.Leonidas, T.K.Maiti, A.Samanta, S.Dasgupta, T.Pathak, S.E.Zographos, and N.G.Oikonomakos (2006).
The binding of 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine to ribonuclease A in the crystal.
  Bioorg Med Chem, 14, 6055-6064.
PDB codes: 2g8q 2g8r
16335788 D.Gaur, and J.K.Batra (2005).
Role of aspartic acid 121 in human pancreatic ribonuclease catalysis.
  Mol Cell Biochem, 275, 95.  
15937284 M.S.Willis, J.K.Hogan, P.Prabhakar, X.Liu, K.Tsai, Y.Wei, and T.Fox (2005).
Investigation of protein refolding using a fractional factorial screen: a study of reagent effects and interactions.
  Protein Sci, 14, 1818-1826.  
15133158 D.Walker, L.Lancaster, R.James, and C.Kleanthous (2004).
Identification of the catalytic motif of the microbial ribosome inactivating cytotoxin colicin E3.
  Protein Sci, 13, 1603-1611.  
15138275 P.M.Leonard, and G.Grogan (2004).
Structure of 6-oxo camphor hydrolase H122A mutant bound to its natural product, (2S,4S)-alpha-campholinic acid: mutant structure suggests an atypical mode of transition state binding for a crotonase homolog.
  J Biol Chem, 279, 31312-31317.
PDB code: 1szo
12773542 M.Zelenina, A.A.Bondar, S.Zelenin, and A.Aperia (2003).
Nickel and extracellular acidification inhibit the water permeability of human aquaporin-3 in lung epithelial cells.
  J Biol Chem, 278, 30037-30043.  
12382288 A.Merlino, L.Vitagliano, M.A.Ceruso, A.Di Nola, and L.Mazzarella (2002).
Global and local motions in ribonuclease A: a molecular dynamics study.
  Biopolymers, 65, 274-283.  
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
11841213 J.L.Brosius, and R.F.Colman (2002).
Three subunits contribute amino acids to the active site of tetrameric adenylosuccinate lyase: Lys268 and Glu275 are required.
  Biochemistry, 41, 2217-2226.  
11478876 E.Notomista, F.Catanzano, G.Graziano, S.Di Gaetano, G.Barone, and A.Di Donato (2001).
Contribution of chain termini to the conformational stability and biological activity of onconase.
  Biochemistry, 40, 9097-9103.  
11331006 R.J.Kubiak, X.Yue, R.J.Hondal, C.Mihai, M.D.Tsai, and K.S.Bruzik (2001).
Involvement of the Arg-Asp-His catalytic triad in enzymatic cleavage of the phosphodiester bond.
  Biochemistry, 40, 5422-5432.  
  21423825 J.M.Messmore, and R.T.Raines (2000).
Pentavalent Organo-Vanadates as Transition State Analogues for Phosphoryl Transfer Reactions.
  J Am Chem Soc, 122, 9911-9916.  
  10892814 L.Vitagliano, A.Merlino, A.Zagari, and L.Mazzarella (2000).
Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2',5')guanosine.
  Protein Sci, 9, 1217-1225.
PDB codes: 1eos 1eow
10632727 T.A.Klink, K.J.Woycechowsky, K.M.Taylor, and R.T.Raines (2000).
Contribution of disulfide bonds to the conformational stability and catalytic activity of ribonuclease A.
  Eur J Biochem, 267, 566-572.  
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.  
10585460 S.A.Krupenko, and C.Wagner (1999).
Aspartate 142 is involved in both hydrolase and dehydrogenase catalytic centers of 10-formyltetrahydrofolate dehydrogenase.
  J Biol Chem, 274, 35777-35784.  
9860854 B.M.Fisher, L.W.Schultz, and R.T.Raines (1998).
Coulombic effects of remote subsites on the active site of ribonuclease A.
  Biochemistry, 37, 17386-17401.
PDB codes: 3rsk 4rsk
9922164 D.J.Quirk, C.Park, J.E.Thompson, and R.T.Raines (1998).
His...Asp catalytic dyad of ribonuclease A: conformational stability of the wild-type, D121N, D121A, and H119A enzymes.
  Biochemistry, 37, 17958-17964.  
  9684895 L.W.Schultz, S.R.Hargraves, T.A.Klink, and R.T.Raines (1998).
Structure and stability of the P93G variant of ribonuclease A.
  Protein Sci, 7, 1620-1625.
PDB code: 3rsp
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.