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PDBsum entry 2k11

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protein links
Hydrolase PDB id
2k11
Jmol
Contents
Protein chain
127 a.a. *
* Residue conservation analysis
PDB id:
2k11
Name: Hydrolase
Title: Solution structure of human pancreatic ribonuclease
Structure: Pancreatic ribonuclease. Chain: a. Synonym: rnase 1, rnase a, rnase upi-1, rib-1, hp-rnase. Engineered: yes
Source: Homo sapiens. Human. Gene: rnase1, rib1, rns1. Expressed in: escherichia coli.
NMR struc: 20 models
Authors: K.E.Kover,M.Bruix,J.Santoro,G.Batta,D.V.Laurents,M.Rico
Key ref:
K.E.Kövér et al. (2008). The solution structure and dynamics of human pancreatic ribonuclease determined by NMR spectroscopy provide insight into its remarkable biological activities and inhibition. J Mol Biol, 379, 953-965. PubMed id: 18495155 DOI: 10.1016/j.jmb.2008.04.042
Date:
20-Feb-08     Release date:   03-Jun-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07998  (RNAS1_HUMAN) -  Ribonuclease pancreatic
Seq:
Struc:
156 a.a.
127 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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   2 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     7 terms  

 

 
DOI no: 10.1016/j.jmb.2008.04.042 J Mol Biol 379:953-965 (2008)
PubMed id: 18495155  
 
 
The solution structure and dynamics of human pancreatic ribonuclease determined by NMR spectroscopy provide insight into its remarkable biological activities and inhibition.
K.E.Kövér, M.Bruix, J.Santoro, G.Batta, D.V.Laurents, M.Rico.
 
  ABSTRACT  
 
Human pancreatic ribonuclease (RNase 1) is expressed in many tissues; has several important enzymatic and biological activities, including efficient cleavage of single-stranded RNA, double-stranded RNA and double-stranded RNA-DNA hybrids, digestion of dietary RNA, regulation of vascular homeostasis, inactivation of the HIV, activation of immature dendritic cells and induction of cytokine production; and furthermore shows potential as an anti-tumor agent. The solution structure and dynamics of uncomplexed, wild-type RNase 1 have been determined by NMR spectroscopy methods to better understand these activities. The family of 20 structures determined on the basis of 6115 unambiguous nuclear Overhauser enhancements is well resolved (pairwise backbone RMSD=1.07 A) and has the classic RNase A type of tertiary structure. Important structural differences compared with previously determined crystal structures of RNase 1 variants or inhibitor-bound complexes are observed in the conformation of loop regions and side chains implicated in the enzymatic as well as biological activities and binding to the cytoplasmic RNase inhibitor. Multiple side chain conformations observed for key surface residues are proposed to be crucial for membrane binding as well as translocation and efficient RNA hydrolysis. (15)N-(1)H relaxation measurements interpreted with the standard and our extended Lipari-Szabo formalism reveal rigid regions and identify more dynamic loop regions. Some of the most dynamic areas are key for binding to the cytoplasmic RNase inhibitor. This finding and the important differences observed between the structure in solution and that bound to the inhibitor are indications that RNase 1 to inhibitor binding can be better described by the "induced fit" model rather than the rigid "lock-into-key" mechanism. Translational diffusion measurements reveal that RNase 1 is predominantly dimeric above 1 mM concentration; the possible implications of this dimeric state for the remarkable biological properties of RNase 1 are discussed.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Representative relaxation data for amide groups of Arg4 (helix α[1]), Val57 (helix α[3]), Gly70 (loop), Met79 (strand β[4]) and Ser127 (C-terminus). (a) T[1] and (b) T[2] values. Lines represent the fits of an exponential decay function to these data sets.
Figure 6.
Fig. 6. Distribution of (a) ^15N CSA values and of (b) HN/CSA axis angles along the RNase 1 sequence.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 379, 953-965) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20197040 A.Kuzmanic, and B.Zagrovic (2010).
Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.
  Biophys J, 98, 861-871.  
  19177350 A.Merlino, G.Avella, S.Di Gaetano, A.Arciello, R.Piccoli, L.Mazzarella, and F.Sica (2009).
Structural features for the mechanism of antitumor action of a dimeric human pancreatic ribonuclease variant.
  Protein Sci, 18, 50-57.
PDB code: 3f8g
19189375 D.V.Laurents, M.Bruix, M.A.Jiménez, J.Santoro, E.Boix, M.Moussaoui, M.V.Nogués, and M.Rico (2009).
The (1)H, (13)C, (15)N resonance assignment, solution structure, and residue level stability of eosinophil cationic protein/RNase 3 determined by NMR spectroscopy.
  Biopolymers, 91, 1018-1028.
PDB code: 2kb5
19459942 G.Batta, T.Barna, Z.Gáspári, S.Sándor, K.E.Kövér, U.Binder, B.Sarg, L.Kaiserer, A.K.Chhillar, A.Eigentler, E.Leiter, N.Hegedüs, I.Pócsi, H.Lindner, and F.Marx (2009).
Functional aspects of the solution structure and dynamics of PAF--a highly-stable antifungal protein from Penicillium chrysogenum.
  FEBS J, 276, 2875-2890.
PDB code: 2kcn
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 code is shown on the right.