PDBsum entry 1jor

Hydrolase

PDB id: 1jor

Contents

Protein chain

149 a.a. *

* Residue conservation analysis

PDB id:

1jor

Name:

Hydrolase

Title:

Ensemble structures for unligated staphylococcal nuclease-h124l

Structure:

Staphylococcal nuclease. Chain: a. Fragment: nuclease a. Synonym: thermonuclease, tnase, micrococcal nuclease. Engineered: yes. Mutation: yes

Source:

Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

30 models

Authors:

J.Wang,D.M.Truckses,F.Abildgaard,Z.Dzakula,Z.Zolnai,J.L.Markley

Key ref:

J.Wang et al. (1997). Solution structures of staphylococcal nuclease from multidimensional, multinuclear NMR: nuclease-H124L and its ternary complex with Ca2+ and thymidine-3',5'-bisphosphate. J Biomol Nmr, 10, 143-164. PubMed id: 9369015

Date:

30-Jul-01 Release date: 22-Aug-01

Protein chain

P00644  (NUC_STAAU) -  Thermonuclease from Staphylococcus aureus

Seq: 231 a.a.

Struc: 149 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.1.31.1 - micrococcal nuclease.
• Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products.

J Biomol Nmr 10:143-164 (1997)

PubMed id: 9369015

Solution structures of staphylococcal nuclease from multidimensional, multinuclear NMR: nuclease-H124L and its ternary complex with Ca2+ and thymidine-3',5'-bisphosphate.

J.Wang, D.M.Truckses, F.Abildgaard, Z.Dzakula, Z.Zolnai, J.L.Markley.

ABSTRACT

The solution structures of staphylococcal nuclease (nuclease) H124L and its ternary complex, (nuclease-H124L).pdTp.Ca2+, were determined by ab initio dynamic simulated annealing using 1925 NOE, 119 phi, 20 chi 1 and 112 hydrogen bond constraints for the free protein, and 2003 NOE, 118 phi, 20 chi 1 and 114 hydrogen bond constraints for the ternary complex. In both cases, the final structures display only small deviations from idealized covalent geometry. In structured regions, the overall root-mean-square deviations from mean atomic coordinates are 0.46 (+/- 0.05) A and 0.41 (+/- 0.05) A for the backbone heavy atoms of nuclease and its ternary complex, respectively. The backbone conformations of residues in the loop formed by Arg81-Gly86, which is adjacent to the active site, are more precisely defined in the ternary complex than in unligated nuclease. Also, the protein side chains that show NOEs and evidence for hydrogen bonds to pdTp (Arg35, Lys84, Tyr85, Arg87, Tyr113, and Tyr115) are better defined in the ternary complex. As has been observed previously in the X-ray structures of nuclease-WT, the binding of pdTp causes the backbone of Tyr113 to change from an extended to a left-handed alpha-helical conformation. The NMR structures reported here were compared with available X-ray structures: nuclease-H124L [Truckses et al. (1996) Protein Sci., 5, 1907-1916] and the ternary complex of wild-type staphylococcal nuclease [Loll and Lattman (1989) Proteins Struct. Funct. Genet., 5, 183-201]. Overall, the solution structures of nuclease-H124L are consistent with these crystal structures, but small differences were observed between the structures in the solution and crystal environments. These included differences in the conformations of certain side chains, a reduction in the extent of helix 1 in solution, and many fewer hydrogen bonds involving side chains in solution.