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PDBsum entry 1c9x

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protein metals links
Hydrolase PDB id
1c9x
Jmol
Contents
Protein chain
124 a.a. *
Metals
_CL ×3
Waters ×103
* Residue conservation analysis
PDB id:
1c9x
Name: Hydrolase
Title: H119a variant of ribonuclease a
Structure: Ribonuclease a. Chain: a. Fragment: ribonuclease a. Engineered: yes. Mutation: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.164    
Authors: C.Park,L.W.Schultz,R.T.Raines
Key ref:
C.Park et al. (2001). Contribution of the active site histidine residues of ribonuclease A to nucleic acid binding. Biochemistry, 40, 4949-4956. PubMed id: 11305910 DOI: 10.1021/bi0100182
Date:
03-Aug-99     Release date:   27-Jun-01    
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 1 residue position (black cross)

 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   4 terms 
  Biochemical function     nucleic acid binding     7 terms  

 

 
DOI no: 10.1021/bi0100182 Biochemistry 40:4949-4956 (2001)
PubMed id: 11305910  
 
 
Contribution of the active site histidine residues of ribonuclease A to nucleic acid binding.
C.Park, L.W.Schultz, R.T.Raines.
 
  ABSTRACT  
 
His12 and His119 are critical for catalysis of RNA cleavage by ribonuclease A (RNase A). Substitution of either residue with an alanine decreases the value of k(cat)/K(M) by more than 10(4)-fold. His12 and His119 are proximal to the scissile phosphoryl group of an RNA substrate in enzyme-substrate complexes. Here, the role of these active site histidines in RNA binding was investigated by monitoring the effect of mutagenesis and pH on the stability of enzyme-nucleic acid complexes. X-ray diffraction analysis of the H12A and H119A variants at a resolution of 1.7 and 1.8 A, respectively, shows that the amino acid substitutions do not perturb the overall structure of the variants. Isothermal titration calorimetric studies on the complexation of wild-type RNase A and the variants with 3'-UMP at pH 6.0 show that His12 and His119 contribute 1.4 and 1.1 kcal/mol to complex stability, respectively. Determination of the stability of the complex of wild-type RNase A and 6-carboxyfluorescein approximately d(AUAA) at varying pHs by fluorescence anisotropy shows that the stability increases by 2.4 kcal/mol as the pH decreases from 8.0 to 4.0. At pH 4.0, replacing His12 with an alanine residue decreases the stability of the complex with 6-carboxyfluorescein approximately d(AUAA) by 2.3 kcal/mol. Together, these structural and thermodynamic data provide the first thorough analysis of the contribution of histidine residues to nucleic acid binding.
 

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
21079871 R.W.Watkins, U.Arnold, and R.T.Raines (2011).
Ribonuclease S redux.
  Chem Commun (Camb), 47, 973-975.  
19921453 D.J.Graham, and J.L.Greminger (2010).
On the information expressed in enzyme primary structure: lessons from Ribonuclease A.
  Mol Divers, 14, 673-686.  
20108951 J.D.Ballin, J.P.Prevas, C.R.Ross, E.A.Toth, G.M.Wilson, and M.T.Record (2010).
Contributions of the histidine side chain and the N-terminal alpha-amino group to the binding thermodynamics of oligopeptides to nucleic acids as a function of pH.
  Biochemistry, 49, 2018-2030.  
19690366 D.Yagi, T.Yamada, K.Kurihara, Y.Ohnishi, M.Yamashita, T.Tamada, I.Tanaka, R.Kuroki, and N.Niimura (2009).
A neutron crystallographic analysis of phosphate-free ribonuclease A at 1.7 A resolution.
  Acta Crystallogr D Biol Crystallogr, 65, 892-899.
PDB code: 3a1r
18001769 J.E.Lee, E.Bae, C.A.Bingman, G.N.Phillips, and R.T.Raines (2008).
Structural basis for catalysis by onconase.
  J Mol Biol, 375, 165-177.
PDB codes: 2gmk 2i5s
17261801 A.Medlock, L.Swartz, T.A.Dailey, H.A.Dailey, and W.N.Lanzilotta (2007).
Substrate interactions with human ferrochelatase.
  Proc Natl Acad Sci U S A, 104, 1789-1793.
PDB codes: 2hrc 2hre
17142283 S.Polydoridis, D.D.Leonidas, N.G.Oikonomakos, and G.Archontis (2007).
Recognition of ribonuclease a by 3'-5'-pyrophosphate-linked dinucleotide inhibitors: a molecular dynamics/continuum electrostatics analysis.
  Biophys J, 92, 1659-1672.  
15475364 B.Ma, and R.Nussinov (2004).
Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes.
  J Biol Chem, 279, 53875-53885.  
12833549 F.Sica, A.Di Fiore, A.Zagari, and L.Mazzarella (2003).
The unswapped chain of bovine seminal ribonuclease: Crystal structure of the free and liganded monomeric derivative.
  Proteins, 52, 263-271.
PDB codes: 1n1x 1n3z
11856829 R.Berisio, F.Sica, V.S.Lamzin, K.S.Wilson, A.Zagari, and L.Mazzarella (2002).
Atomic resolution structures of ribonuclease A at six pH values.
  Acta Crystallogr D Biol Crystallogr, 58, 441-450.
PDB codes: 1kf2 1kf3 1kf4 1kf5 1kf7 1kf8
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.