PDBsum entry 4j5k

Hydrolase

PDB id: 4j5k

Contents

Protein chains

96 a.a.

Ligands

SO4

GOL ×2

Waters ×419

PDB id:

4j5k

Name:

Hydrolase

Title:

Crystal structure analysis of streptomyces aureofaciens ribonuclease sa y51f mutant

Structure:

Guanyl-specific ribonuclease sa. Chain: a, b. Fragment: ribonuclease sa. Synonym: rnase sa. Engineered: yes. Mutation: yes

Source:

Streptomyces aureofaciens. Organism_taxid: 1894. Strain: bmk. Gene: rnasa. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.23Å R-factor: 0.106 R-free: 0.136

Authors:

L.Urbanikova,J.Sevcik

Key ref:

C.N.Pace et al. (2014). Contribution of hydrogen bonds to protein stability. Protein Sci, 23, 652-661. PubMed id: 24591301 DOI: 10.1002/pro.2449

Date:

08-Feb-13 Release date: 28-May-14

Protein chains

P05798  (RNSA_KITAU) -  Guanyl-specific ribonuclease Sa from Kitasatospora aureofaciens

Seq: 96 a.a.

Struc: 96 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.6.1.24 - ribonuclease T1.
• Reaction: [RNA] containing guanosine + H2O = an [RNA fragment]-3'-guanosine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]

DOI no: 10.1002/pro.2449

Protein Sci 23:652-661 (2014)

PubMed id: 24591301

Contribution of hydrogen bonds to protein stability.

C.N.Pace, H.Fu, K.Lee Fryar, J.Landua, S.R.Trevino, D.Schell, R.L.Thurlkill, S.Imura, J.M.Scholtz, K.Gajiwala, J.Sevcik, L.Urbanikova, J.K.Myers, K.Takano, E.J.Hebert, B.A.Shirley, G.R.Grimsley.

ABSTRACT

Our goal was to gain a better understanding of the contribution of the burial of polar groups and their hydrogen bonds to the conformational stability of proteins. We measured the change in stability, Δ(ΔG), for a series of hydrogen bonding mutants in four proteins: villin headpiece subdomain (VHP) containing 36 residues, a surface protein from Borrelia burgdorferi (VlsE) containing 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa (RNase Sa) and T1 (RNase T1). Crystal structures were determined for three of the hydrogen bonding mutants of RNase Sa: S24A, Y51F, and T95A. The structures are very similar to wild type RNase Sa and the hydrogen bonding partners form intermolecular hydrogen bonds to water in all three mutants. We compare our results with previous studies of similar mutants in other proteins and reach the following conclusions. (1) Hydrogen bonds contribute favorably to protein stability. (2) The contribution of hydrogen bonds to protein stability is strongly context dependent. (3) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (4) Polar group burial can make a favorable contribution to protein stability even if the polar groups are not hydrogen bonded. (5) The contribution of hydrogen bonds to protein stability is similar for VHP, a small protein, and VlsE, a large protein.