PDBsum entry 1rhb

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Hydrolase (nucleic acid,RNA) PDB id
Protein chain
124 a.a. *
Waters ×160
* Residue conservation analysis
PDB id:
Name: Hydrolase (nucleic acid,RNA)
Title: Water dependent domain motion and flexibility in ribonuclease a and the invariant features in its hydration shell. An x-ray study of two low humidity crystal forms of the enzyme
Structure: Ribonuclease a. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Cell_line: s2. Organ: pancreas
1.50Å     R-factor:   0.173    
Authors: K.V.Radha Kishan,N.R.Chandra,C.Sudarsanakumar,K.Suguna, M.Vijayan
Key ref:
R.V.Kishan et al. (1995). Water-dependent domain motion and flexibility in ribonuclease A and the invariant features in its hydration shell. An X-ray study of two low-humidity crystal forms of the enzyme. Acta Crystallogr D Biol Crystallogr, 51, 703-710. PubMed id: 15299799 DOI: 10.1107/S0907444994014794
13-Nov-94     Release date:   27-Feb-95    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
150 a.a.
124 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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: 10.1107/S0907444994014794 Acta Crystallogr D Biol Crystallogr 51:703-710 (1995)
PubMed id: 15299799  
Water-dependent domain motion and flexibility in ribonuclease A and the invariant features in its hydration shell. An X-ray study of two low-humidity crystal forms of the enzyme.
R.V.Kishan, N.R.Chandra, C.Sudarsanakumar, K.Suguna, M.Vijayan.
The crystal structures of 88 and 79% relative humidity forms of ribonuclease A, resulting from water-mediated transformations, have been refined employing the restrained least-squares method using X-ray data collected on an area detector to R = 0.173 for 15 326 observed reflections in the 10-1.5 A resolution shell and R = 0.176 for 8534 observed reflections in the 10-1.8 A shell, respectively. The comparison of these structures with those of the native, the phosphate-bound and the sulfate-bound forms demonstrates that the mobility of the ribonuclease A molecule involves hinge-bending movement of the two domains and local flexibility within them, particularly at the termini of regular secondary structures and in loops. The comparison also leads to the identification of 31 invariant water molecules in the hydration shell of the enzyme, many of which are involved in holding different parts of the molecule together and in stabilizing local structure. The conformational changes that accompany the partial removal of the surrounding water, particularly those observed in the 79% form, could be similar to those that occur during enzyme action.
  Selected figure(s)  
Figure 2.
Fig. 2. Ca representations of the molecule in the native (unbroken line) and the 79% (broken line) forms. The A domains in the two stuctues have been superpose.
Figure 5.
Fig. 5. Invariant water molecules that bridge (a) the N-terminal heli ad the C-terminal strand and the preceding loop, and (b) the 24-33 helix and the 94-100 strand.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1995, 51, 703-710) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20124705 S.B.Larson, J.S.Day, C.Nguyen, R.Cudney, and A.McPherson (2010).
Structure of bovine pancreatic ribonuclease complexed with uridine 5'-monophosphate at 1.60 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 113-120.
PDB code: 3jw1
19544573 A.Sharma, K.Sekar, and M.Vijayan (2009).
Structure, dynamics, and interactions of jacalin. Insights from molecular dynamics simulations examined in conjunction with results of X-ray studies.
  Proteins, 77, 760-777.  
17932936 L.Vijayalakshmi, R.Krishna, R.Sankaranarayanan, and M.Vijayan (2008).
An asymmetric dimer of beta-lactoglobulin in a low humidity crystal form--structural changes that accompany partial dehydration and protein action.
  Proteins, 71, 241-249.
PDB codes: 2q2m 2q2p 2q39
  18540052 P.S.Kaushal, R.Sankaranarayanan, and M.Vijayan (2008).
Water-mediated variability in the structure of relaxed-state haemoglobin.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 463-469.
PDB codes: 2zlt 2zlu 2zlv 2zlw 2zlx
  17277440 V.Venugopal, B.Sen, A.K.Datta, and R.Banerjee (2007).
Structure of cyclophilin from Leishmania donovani at 1.97 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 60-64.
PDB code: 2haq
12945053 A.Merlino, L.Vitagliano, M.A.Ceruso, and L.Mazzarella (2003).
Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin.
  Proteins, 53, 101-110.  
11746706 L.Vitagliano, A.Merlino, A.Zagari, and L.Mazzarella (2002).
Reversible substrate-induced domain motions in ribonuclease A.
  Proteins, 46, 97.
PDB codes: 1jvt 1jvu 1jvv
  10548049 J.A.Bell (1999).
X-ray crystal structures of a severely desiccated protein.
  Protein Sci, 8, 2033-2040.
PDB codes: 1c0b 1c0c
  10082366 L.Vitagliano, S.Adinolfi, A.Riccio, F.Sica, A.Zagari, and L.Mazzarella (1998).
Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine.
  Protein Sci, 7, 1691-1699.
PDB code: 11ba
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