PDBsum entry 1rpg

Hydrolase(phosphoric diester)

PDB id: 1rpg

Contents

Protein chain

124 a.a. *

Ligands

CPA

MPD

Waters ×164

* Residue conservation analysis

PDB id:

1rpg

Name:

Hydrolase(phosphoric diester)

Title:

Structures of rnase a complexed with 3'-cmp and d(cpa): active site conformation and conserved water molecules

Structure:

Ribonuclease a. Chain: a. Engineered: yes

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Cell_line: s2. Organ: pancreas

Resolution:

1.40Å R-factor: 0.172

Authors:

I.Zegers,L.Wyns,R.Palmer

Key ref:

I.Zegers et al. (1994). The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules. Protein Sci, 3, 2322-2339. PubMed id: 7756988 DOI: 10.1002/pro.5560031217

Date:

29-Aug-94 Release date: 20-Dec-94

Protein chain

P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic from Bos taurus

Seq: 150 a.a.

Struc: 124 a.a.

Enzyme reactions

• Enzyme class: E.C.4.6.1.18 - pancreatic ribonuclease.
• Reaction:
  1. an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]
  2. an [RNA] containing uridine + H2O = an [RNA]-3'-uridine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]

DOI no: 10.1002/pro.5560031217

Protein Sci 3:2322-2339 (1994)

PubMed id: 7756988

The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules.

I.Zegers, D.Maes, M.H.Dao-Thi, F.Poortmans, R.Palmer, L.Wyns.

ABSTRACT

The interactions of RNase A with cytidine 3'-monophosphate (3'-CMP) and deoxycytidyl-3',5'-deoxyadenosine (d(CpA)) were analyzed by X-ray crystallography. The 3'-CMP complex and the native structure were determined from trigonal crystals, and the d(CpA) complex from monoclinic crystals. The differences between the overall structures are concentrated in loop regions and are relatively small. The protein-inhibitor contacts are interpreted in terms of the catalytic mechanism. The general base His 12 interacts with the 2' oxygen, as does the electrostatic catalyst Lys 41. The general acid His 119 has 2 conformations (A and B) in the native structure and is found in, respectively, the A and the B conformation in the d(CpA) and the 3'-CMP complex. From the present structures and from a comparison with RNase T1, we propose that His 119 is active in the A conformation. The structure of the d(CpA) complex permits a detailed analysis of the downstream binding site, which includes His 119 and Asn 71. The comparison of the present RNase A structures with an inhibitor complex of RNase T1 shows that there are important similarities in the active sites of these 2 enzymes, despite the absence of any sequence homology. The water molecules were analyzed in order to identify conserved water sites. Seventeen water sites were found to be conserved in RNase A structures from 5 different space groups. It is proposed that 7 of those water molecules play a role in the binding of the N-terminal helix to the rest of the protein and in the stabilization of the active site.

Selected figure(s)

Figure 2.
IRPF P3221 2.2 116 15.5 pH 6, (NH4)2S04, NaCl 4SRN P3221 2.0 105 20.4 pH5.2,(NH4)2S04, CSCI

Figure 4.
RPF 4SRN

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1994, 3, 2322-2339) copyright 1994.

Figures were selected by an automated process.