PDBsum entry 2fg7

Transferase

PDB id: 2fg7

Contents

Protein chains

(+ 0 more) 321 a.a. *

Ligands

SO4 ×2

SN0 ×6

_CP ×6

Waters ×265

* Residue conservation analysis

PDB id:

2fg7

Name:

Transferase

Title:

N-succinyl-l-ornithine transcarbamylase from b. Fragilis complexed with carbamoyl phosphate and n-succinyl-l-norvaline

Structure:

Putative ornithine carbamoyltransferase. Chain: x, y, z, c, d, e. Engineered: yes. Mutation: yes

Source:

Bacteroides fragilis. Organism_taxid: 272559. Strain: nctc 9343. Gene: argf'. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Trimer (from PQS)

Resolution:

2.90Å R-factor: 0.204 R-free: 0.229

Authors:

D.Shi,X.Yu,M.H.Malamy,N.M.Allewell,M.Tuchman

Key ref:

D.Shi et al. (2006). Structure and catalytic mechanism of a novel N-succinyl-L-ornithine transcarbamylase in arginine biosynthesis of Bacteroides fragilis. J Biol Chem, 281, 20623-20631. PubMed id: 16704984 DOI: 10.1074/jbc.M601229200

Date:

21-Dec-05 Release date: 23-May-06

Protein chains

Q5LI27  (Q5LI27_BACFN) -  N-succinylornithine carbamoyltransferase from Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow)

Seq: 318 a.a.

Struc: 322 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.1.3.11 - N-succinylornithine carbamoyltransferase.
• Reaction: N₂-succinyl-L-ornithine + carbamoyl phosphate = N₂-succinyl-L- citrulline + phosphate + H⁺

N(2)-succinyl-L-ornithine (Bound ligand (Het Group name = CP) corresponds exactly) + carbamoyl phosphate (Bound ligand (Het Group name = SN0) matches with 93.75% similarity) = N(2)-succinyl-L- citrulline + phosphate + H(+)

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

reference

DOI no: 10.1074/jbc.M601229200

J Biol Chem 281:20623-20631 (2006)

PubMed id: 16704984

Structure and catalytic mechanism of a novel N-succinyl-L-ornithine transcarbamylase in arginine biosynthesis of Bacteroides fragilis.

D.Shi, H.Morizono, J.Cabrera-Luque, X.Yu, L.Roth, M.H.Malamy, N.M.Allewell, M.Tuchman.

ABSTRACT

A Bacteroides fragilis gene (argF'(bf)), the disruption of which renders the bacterium auxotrophic for arginine, was expressed and its recombinant protein purified and studied. The novel protein catalyzes the carbamylation of N-succinyl-L-ornithine but not L-ornithine or N-acetyl-L-ornithine, forming N-succinyl-L-citrulline. Crystal structures of this novel transcarbamylase complexed with carbamyl phosphate and N-succinyl-L-norvaline, as well as sulfate and N-succinyl-L-norvaline have been determined and refined to 2.9 and 2.8 A resolution, respectively. They provide structural evidence that this protein is a novel N-succinyl-L-ornithine transcarbamylase. The data provided herein suggest that B. fragilis uses N-succinyl-L-ornithine rather than N-acetyl-L-ornithine for de novo arginine biosynthesis and therefore that this pathway in Bacteroides is different from the canonical arginine biosynthetic pathway of most organisms. Comparison of the structures of the new protein with those recently reported for N-acetyl-L-ornithine transcarbamylase indicates that amino acid residue 90 (B. fragilis numbering) plays an important role in conferring substrate specificity for N-succinyl-L-ornithine versus N-acetyl-L-ornithine. Movement of the 120 loop upon substrate binding occurs in N-succinyl-L-ornithine transcarbamylase, while movement of the 80 loop and significant domain closure take place as in other transcarbamylases. These findings provide new information on the putative role of succinylated intermediates in arginine biosynthesis and on the evolution of transcarbamylases.

Selected figure(s)

Figure 1.
Contours of the electron density maps (2F[o] - F[c]) (1.0 σ shown in blue cage) at 2.8 and 2.9 Å resolution for the SO[4]+SNO-bound (left) and CP+SNO-bound structures (right), respectively.

Figure 4.
Active site of SOTCase. The final refined positions of the ligands are represented as colored sticks. A, stereo view showing the active site of B. fragilis CP+SNO-bound SOTCase. Interactions of active site residues with bound CP and SNO (yellow stick) are illustrated in pink dashed lines. Residue Trp^75 indicated by ^* is from an adjacent monomer. B, comparison of the active sites of SOTCase (left) and AOTCase (right) near the succinyl group. SNO and N-acetylcitrulline are shown as thick ball-and-stick models, while the surrounding residues are shown as thin ball-and-stick models. Residue Pro^90 in SOTCase from the adjacent subunit (equivalent to Glu^92 in AOTCase) shown in red is the residue that distinguishes SOTCase from AOTCase. Coordinates of AOTCase are taken from PDB 1YH1.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 20623-20631) copyright 2006.

Figures were selected by an automated process.