4RSK

STRUCTURE OF THE K7A/R10A/K66A VARIANT OF RIBONUCLEASE A COMPLEXED WITH 3'-UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Coulombic Effects of Remote Subsites on the Active Site of Ribonuclease A

Fisher, B.M.Schultz, L.W.Raines, R.T.

(1998) Biochemistry 37: 17386-17401

  • DOI: 10.1021/bi981369s
  • Primary Citation of Related Structures:  
    3RSK, 4RSK

  • PubMed Abstract: 
  • The active-site cleft of bovine pancreatic ribonuclease A (RNase A) is lined with cationic residues that interact with a bound nucleic acid. Those residues interacting with the phosphoryl groups comprise the P0, P1, and P2 subsites, with the scissile P-O5' bond residing in the P1 subsite ...

    The active-site cleft of bovine pancreatic ribonuclease A (RNase A) is lined with cationic residues that interact with a bound nucleic acid. Those residues interacting with the phosphoryl groups comprise the P0, P1, and P2 subsites, with the scissile P-O5' bond residing in the P1 subsite. Coulombic interactions between the P0 and P2 subsites and phosphoryl groups of the substrate were characterized previously [Fisher, B. M., Ha, J.-H., and Raines, R. T. (1998) Biochemistry 37, 12121-12132]. Here, the interactions between these subsites and the active-site residues His12 and His119 are described in detail. A protein variant in which the cationic residues in these subsites (Lys66 in the P0 subsite and Lys7 and Arg10 in the P2 subsite) were replaced with alanine was crystallized, both free and with bound 3'-uridine monophosphate (3'-UMP). Structures of K7A/R10A/K66A RNase A and the K7A/R10A/K66A RNase A.3'-UMP complex were determined by X-ray diffraction analysis to resolutions of 2.0 and 2.1 A, respectively. There is little observable change between these structures and that of wild-type RNase A, either free or with bound 3'-cytidine monophosphate. K7A/R10A/K66A RNase A was evaluated for its ability to cleave UpA, a dinucleotide substrate that does not span the P0 or the P2 subsites. In comparison to the wild-type enzyme, the value of kcat was decreased by 5-fold and that of kcat/Km was decreased 10-fold, suggesting that these remote subsites interact with the active site. These interactions were characterized by determining the pKa values of His12 and His119 at 0.018 and 0.142 M Na+, both in wild-type RNase A and the K7A/R10A/K66A variant. The side chains of Lys7, Arg10, and Lys66 depress the pKa values of these histidine residues, and this depression is sensitive to the salt concentration. In addition, the P0 and P2 subsites influence the interaction of His12 and His119 with each other, as demonstrated by changes in the cooperativity that gives rise to microscopic pKa values. Finally, the affinity of 3'-UMP for wild-type RNase A and the K7A/R10A/K66A variant at 0.018 and 0.142 M Na+ was determined by isothermal titration calorimetry. 3'-UMP binds to the variant protein with 5-fold weaker affinity at 0.018 M Na+ and 3-fold weaker affinity at 0.142 M Na+ than it binds to wild-type RNase A. Together these data demonstrate that long-range Coulombic interactions are an important feature in catalysis by RNase A.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison 53706, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASE AA124Bos taurusMutation(s): 3 
Gene Names: RNASE1RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U3P (Subject of Investigation/LOI)
Query on U3P

Download Ideal Coordinates CCD File 
B [auth A]3'-URIDINEMONOPHOSPHATE
C9 H13 N2 O9 P
FOGRQMPFHUHIGU-XVFCMESISA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
U3P BindingDB:  4RSK Ki: min: 7.85e+4, max: 8.20e+4 (nM) from 2 assay(s)
Binding MOAD:  4RSK Kd: 4.74e+4 (nM) from 1 assay(s)
PDBBind:  4RSK Kd: 4.74e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.62α = 90
b = 69.62β = 90
c = 66.98γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
XCALIBREdata reduction
TNTrefinement
XDSdata reduction
XCALIBREdata scaling
TNTphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-12-09
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations