PDBsum entry 2pb2

Transferase

PDB id: 2pb2

Contents

Protein chains

378 a.a. *

Ligands

PLP

EDO ×6

GOL

Waters ×573

* Residue conservation analysis

PDB id:

2pb2

Name:

Transferase

Title:

Structure of biosynthetic n-acetylornithine aminotransferase from salmonella typhimurium: studies on substrate specificity and inhibitor binding

Structure:

Acetylornithine/succinyldiaminopimelate aminotransferase. Chain: a, b. Synonym: acoat, succinyldiaminopimelate transferase, dapatase. Engineered: yes

Source:

Salmonella typhimurium. Organism_taxid: 99287. Strain: lt2. Gene: argd. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.91Å R-factor: 0.198 R-free: 0.237

Authors:

V.Rajaram,P.Ratna Prasuna,H.S.Savithri,M.R.N.Murthy

Key ref:

V.Rajaram et al. (2008). Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium: studies on substrate specificity and inhibitor binding. Proteins, 70, 429-441. PubMed id: 17680699 DOI: 10.1002/prot.21567

Date:

28-Mar-07 Release date: 25-Dec-07

Protein chains

P40732  (ARGD_SALTY) -  Acetylornithine/succinyldiaminopimelate aminotransferase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

Seq: 405 a.a.

Struc: 378 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.6.1.11 - acetylornithine transaminase.
• Pathway: Ornithine Biosynthesis
• Reaction: N₂-acetyl-L-ornithine + 2-oxoglutarate = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate

N(2)-acetyl-L-ornithine (Bound ligand (Het Group name = GOL) matches with 45.45% similarity) + 2-oxoglutarate = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate

• Cofactor: Pyridoxal 5'-phosphate

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

• Enzyme class 2: E.C.2.6.1.17 - succinyldiaminopimelate transaminase.

Pathway:

• Reaction: N-succinyl-(2S,6S)-2,6-diaminopimelate + 2-oxoglutarate = (S)-2- succinylamino-6-oxoheptanedioate + L-glutamate

N-succinyl-(2S,6S)-2,6-diaminopimelate (Bound ligand (Het Group name = GOL) matches with 45.45% similarity) + 2-oxoglutarate = (S)-2- succinylamino-6-oxoheptanedioate + L-glutamate

• 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: 10.1002/prot.21567

Proteins 70:429-441 (2008)

PubMed id: 17680699

Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium: studies on substrate specificity and inhibitor binding.

V.Rajaram, P.Ratna Prasuna, H.S.Savithri, M.R.Murthy.

ABSTRACT

Acetylornithine aminotransferase (AcOAT) is one of the key enzymes involved in arginine metabolism and catalyzes the conversion of N-acetylglutamate semialdehyde to N-acetylornithine (AcOrn) in the presence of L-glutamate. It belongs to the Type I subgroup II family of pyridoxal 5'-phosphate (PLP) dependent enzymes. E. coli biosynthetic AcOAT (eAcOAT) also catalyzes the conversion of N-succinyl-L-2-amino-6-oxopimelate to N-succinyl-L,L-diaminopimelate, one of the steps in lysine biosynthesis. In view of the critical role of AcOAT in lysine and arginine biosynthesis, structural studies were initiated on the enzyme from S. typhimurium (sAcOAT). The K(m) and k(cat)/K(m) values determined with the purified sAcOAT suggested that the enzyme had much higher affinity for AcOrn than for ornithine (Orn) and was more efficient than eAcOAT. sAcOAT was inhibited by gabaculine (Gcn) with an inhibition constant (K(i)) of 7 microM and a second-order rate constant (k(2)) of 0.16 mM(-1) s(-1). sAcOAT, crystallized in the unliganded form and in the presence of Gcn or L-glutamate, diffracted to a maximum resolution of 1.90 A and contained a dimer in the asymmetric unit. The structure of unliganded sAcOAT showed significant electron density for PLP in only one of the subunits (subunit A). The asymmetry in PLP binding could be attributed to the ordering of the loop L(alphak-) (betam) in only one subunit (subunit B; the loop from subunit B comes close to the phosphate group of PLP in subunit A). Structural and spectral studies of sAcOAT with Gcn suggested that the enzyme might have a low affinity for PLP-Gcn complex. Comparison of sAcOAT with T. thermophilus AcOAT and human ornithine aminotransferase suggested that the higher specificity of sAcOAT towards AcOrn may not be due to specific changes in the active site residues but could result from minor conformational changes in some of them. This is the first structural report of AcOAT from a mesophilic organism and could serve as a basis for drug design as the enzyme is important for bacterial cell wall biosynthesis.

Selected figure(s)

Figure 1.
Figure 1. (a) Reaction catalyzed by AcOAT in arginine biosynthesis. (b) Reaction catalyzed by AcOAT in lysine biosynthesis. (c) Reaction of Gcn with PLP leading to the formation of a Schiff base followed by proton abstraction and aromatization to form m-carboxyphenylpyridoamine phosphate (CPPP).

Figure 9.
Figure 9. (a) Stereo view of electron density corresponding to PLP in the active site of subunit A of sAcOAT-IA from the final F[o]-F[c] map contoured at 3 . Hydrogen-bonding interactions of PLP with the enzyme are shown as dotted lines. (b) Stereo view of electron density corresponding to PLP in the active site of subunit A of sAcOAT-GCN in the final F[o]-F[c] map contoured at 3 . PLP in sAcOAT-GCN is shown in light gray as a ball and stick model and PLP from sAcOAT-IA is shown in dark gray. The small tilt in orientation (7°) with respect to each other may be observed.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 70, 429-441) copyright 2008.

Figures were selected by an automated process.