PDBsum entry 1sjb

Lyase, isomerase

PDB id: 1sjb

Contents

Protein chains

367 a.a. *

Ligands

OSB ×4

Metals

_MG ×4

Waters ×774

* Residue conservation analysis

PDB id:

1sjb

Name:

Lyase, isomerase

Title:

X-ray structure of o-succinylbenzoate synthase complexed with o- succinylbenzoic acid

Structure:

N-acylamino acid racemase. Chain: a, b, c, d. Synonym: o-succinylbenzoate synthase. Engineered: yes

Source:

Amycolatopsis sp.. Organism_taxid: 37632. Gene: aaar. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Octamer (from PDB file)

Resolution:

2.20Å R-factor: 0.209 R-free: 0.272

Authors:

J.B.Thoden,E.A.Taylor-Ringia,J.B.Garrett,J.A.Gerlt,H.M.Holden, I.Rayment

Key ref:

J.B.Thoden et al. (2004). Evolution of enzymatic activity in the enolase superfamily: structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis. Biochemistry, 43, 5716-5727. PubMed id: 15134446 DOI: 10.1021/bi0497897

Date:

03-Mar-04 Release date: 01-Jun-04

Protein chains

Q44244  (NSAR_AMYSP) -  N-succinylamino acid racemase from Amycolatopsis sp

Seq: 368 a.a.

Struc: 367 a.a.

Enzyme reactions

• Enzyme class 1: E.C.4.2.1.113 - o-succinylbenzoate synthase.
• Reaction: (1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O

(1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate (Bound ligand (Het Group name = OSB) corresponds exactly) + H2O

• Cofactor: Mn(2+) or Mg(2+)
• Enzyme class 2: E.C.5.1.1.- - ?????

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

Added reference

DOI no: 10.1021/bi0497897

Biochemistry 43:5716-5727 (2004)

PubMed id: 15134446

Evolution of enzymatic activity in the enolase superfamily: structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis.

J.B.Thoden, E.A.Taylor Ringia, J.B.Garrett, J.A.Gerlt, H.M.Holden, I.Rayment.

ABSTRACT

Divergent evolution of enzyme function is commonly explained by a gene duplication event followed by mutational changes that allow the protein encoded by the copy to acquire a new function. An alternate hypothesis is that this process is facilitated when the progenitor enzyme acquires a second function while maintaining the original activity. This phenomenon has been suggested to occur in the o-succinylbenzoate synthase (OSBS) from a species of Amycolatopsis that catalyzes not only the physiological syn-dehydration reaction of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate but also an accidental racemization of N-acylamino acids [Palmer, D. R., Garrett, J. B., Sharma, V., Meganathan, R., Babbitt, P. C., and Gerlt, J. A. (1999) Biochemistry 38, 4252-4258]. To understand the molecular basis of this promiscuity, three-dimensional structures of liganded complexes of this enzyme have been determined, including the product of the OSBS reaction and three N-acylamino acid substrates for the N-acylamino acid racemase (NAAAR) reaction, N-acetylmethionine, N-succinylmethionine, and N-succinylphenylglycine, to 2.2, 2.3, 2.1, and 1.9 A resolution, respectively. These structures show how the active-site cavity can accommodate both the hydrophobic substrate for the OSBS reaction and the substrates for the accidental NAAAR reaction. As expected, the N-acylamino acid is sandwiched between lysines 163 and 263, which function as the catalytic bases for the abstraction of the alpha-proton in the (R)- and (S)-racemization reactions, respectively [Taylor Ringia, E. A., Garrett, J. B, Thoden, J. B., Holden, H. M., Rayment, I., and Gerlt, J. A. (2004) Biochemistry 42, 224-229]. Importantly, the protein forms specific favorable interactions with the hydrophobic amino acid side chain, alpha-carbon, carboxylate, and the polar components of the N-acyl linkage. Accommodation of the components of the N-acyl linkage appears to be the reason that this enzyme is capable of a racemization reaction on these substrates, whereas the orthologous OSBS from Escherichia coli lacks this functionality.