PDBsum entry 1wkv

Transferase

PDB id: 1wkv

Contents

Protein chains

382 a.a. *

Ligands

ACT ×2

PLP ×2

Waters ×634

* Residue conservation analysis

PDB id:

1wkv

Name:

Transferase

Title:

Crystal structure of o-phosphoserine sulfhydrylase

Structure:

Cysteine synthase. Chain: a, b. Synonym: o-phosphoserine sulfhydrylase. Engineered: yes

Source:

Aeropyrum pernix. Organism_taxid: 272557. Strain: k1. Gene: ape1586. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.190 R-free: 0.231

Authors:

Y.Oda,K.Mino,K.Ishikawa,M.Ataka

Key ref:

Y.Oda et al. (2005). Three-dimensional structure of a new enzyme, O-phosphoserine sulfhydrylase, involved in l-cysteine biosynthesis by a hyperthermophilic archaeon, Aeropyrum pernix K1, at 2.0A resolution. J Mol Biol, 351, 334-344. PubMed id: 16005886 DOI: 10.1016/j.jmb.2005.05.064

Date:

09-Jun-04 Release date: 28-Jun-05

Protein chains

Q9YBL2  (CYSO_AERPE) -  Protein CysO from Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)

Seq: 389 a.a.

Struc: 382 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.5.1.47 - cysteine synthase.
• Reaction: O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate

O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate (Bound ligand (Het Group name = ACT) corresponds exactly)

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

• Enzyme class 2: E.C.2.5.1.65 - O-phosphoserine sulfhydrylase.
• Reaction: O-phospho-L-serine + hydrogen sulfide + H⁺ = L-cysteine + phosphate

O-phospho-L-serine + hydrogen sulfide + H(+) = L-cysteine (Bound ligand (Het Group name = ACT) matches with 57.14% similarity) + phosphate

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

• Enzyme class 3: E.C.4.2.1.22 - cystathionine beta-synthase.
• Reaction: L-homocysteine + L-serine = L,L-cystathionine + H2O

L-homocysteine + L-serine (Bound ligand (Het Group name = ACT) matches with 57.14% similarity) = L,L-cystathionine + H2O

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2005.05.064

J Mol Biol 351:334-344 (2005)

PubMed id: 16005886

Three-dimensional structure of a new enzyme, O-phosphoserine sulfhydrylase, involved in l-cysteine biosynthesis by a hyperthermophilic archaeon, Aeropyrum pernix K1, at 2.0A resolution.

Y.Oda, K.Mino, K.Ishikawa, M.Ataka.

ABSTRACT

O-Phosphoserine sulfhydrylase is a new enzyme found in a hyperthermophilic archaeon, Aeropyrum pernix K1. This enzyme catalyzes a novel cysteine synthetic reaction from O-phospho-l-serine and sulfide. The crystal structure of the enzyme was determined at 2.0A resolution using the method of multi-wavelength anomalous dispersion. A monomer consists of three domains, including an N-terminal domain with a new alpha/beta fold. The topology folds of the middle and C-terminal domains were similar to those of the O-acetylserine sulfhydrylase-A from Salmonella typhimurium and the cystathionine beta-synthase from human. The cofactor, pyridoxal 5'-phosphate, is bound in a cleft between the middle and C-terminal domains through a covalent linkage to Lys127. Based on the structure determined, O-phospho-l-serine could be rationally modeled into the active site of the enzyme. An enzyme-substrate complex model and a mutation experiment revealed that Arg297, unique to hyperthermophilic archaea, is one of the most crucial residues for O-phosphoserine sulfhydrylation activity. There are more hydrophobic areas and less electric charges at the dimer interface, compared to the S.typhimurium O-acetylserine sulfhydrylase.

Selected figure(s)

Figure 2.
Figure 2. A detailed structure of the active site of OPSS. (a) Stereo view of the active site region of OPSS. The cofactor PLP and the bound acetate ion are located at the center of the active site. Their 2F[o] -F[c] electron density is shown at 2s. Hydrogen bonds are shown as broken lines. A Schiff base linkage is shown as a thick, broken blue line. (b) A schematic of hydrogen bond interactions among PLP moiety, protein and water molecules. (c) Stereo view of a proposed model of the OPSS active site with phosphoserine. Phosphoserine was built into the active site to make a Schiff base linkage with PLP and to bind with Thr152, Ser153, and Gln224. The negative charge of the phosphate group of phosphoserine is presumably interacting with Arg297. The Figure was produced with MOLSCRIPT.29

Figure 4.
Figure 4. Stereo views of comparisons of the active site regions between OPSS and S. typhimurium OASS or human CBS. (a) A superposition of OPSS (green) and the mutant OASS bound with methionine (gray). (b) A superposition of OPSS (green) and the free form of wild-type OASS (gray). (c) A superposition of OPSS (green) and CBS (gray). In CBS, a residue corresponding to Thr203 of OPSS is not visible in its crystallographic structure. The Figure was produced with MOLSCRIPT29 and Raster3D.30

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 351, 334-344) copyright 2005.

Figures were selected by an automated process.