PDBsum entry 1amu

Peptide synthetase

PDB id: 1amu

Contents

Protein chains

509 a.a. *

Ligands

SO4 ×2

PHE ×2

AMP ×2

Metals

_MG ×2

Waters ×569

* Residue conservation analysis

PDB id:

1amu

Name:

Peptide synthetase

Title:

Phenylalanine activating domain of gramicidin synthetase 1 in a complex with amp and phenylalanine

Structure:

Gramicidin synthetase 1. Chain: a, b. Fragment: adenylate forming domain, residues 1 - 556 plus a 7 residuE C-terminal tag - shhhhhh. Synonym: grsa. Engineered: yes

Source:

Brevibacillus brevis. Organism_taxid: 1393. Collection: atcc 999. Gene: grsa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.213 R-free: 0.246

Authors:

E.Conti,T.Stachelhaus,M.A.Marahiel,P.Brick

Key ref:

E.Conti et al. (1997). Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S. Embo J, 16, 4174-4183. PubMed id: 9250661 DOI: 10.1093/emboj/16.14.4174

Date:

18-Jun-97 Release date: 01-Jul-98

Protein chains

P0C061  (GRSA_ANEMI) -  Gramicidin S synthase 1 from Aneurinibacillus migulanus

Seq: 1098 a.a.

Struc: 509 a.a.

Enzyme reactions

• Enzyme class: E.C.5.1.1.11 - phenylalanine racemase (ATP-hydrolyzing).
• Reaction: L-phenylalanine + ATP + H2O = D-phenylalanine + AMP + diphosphate + H⁺

L-phenylalanine + ATP + H2O (Bound ligand (Het Group name = PHE) corresponds exactly) = D-phenylalanine (Bound ligand (Het Group name = AMP) corresponds exactly) + AMP + diphosphate + H(+)

• Cofactor: Pyridoxal 5'-phosphate

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

reference

DOI no: 10.1093/emboj/16.14.4174

Embo J 16:4174-4183 (1997)

PubMed id: 9250661

Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S.

E.Conti, T.Stachelhaus, M.A.Marahiel, P.Brick.

ABSTRACT

The non-ribosomal synthesis of the cyclic peptide antibiotic gramicidin S is accomplished by two large multifunctional enzymes, the peptide synthetases 1 and 2. The enzyme complex contains five conserved subunits of approximately 60 kDa which carry out ATP-dependent activation of specific amino acids and share extensive regions of sequence similarity with adenylating enzymes such as firefly luciferases and acyl-CoA ligases. We have determined the crystal structure of the N-terminal adenylation subunit in a complex with AMP and L-phenylalanine to 1.9 A resolution. The 556 amino acid residue fragment is folded into two domains with the active site situated at their interface. Each domain of the enzyme has a similar topology to the corresponding domain of unliganded firefly luciferase, but a remarkable relative domain rotation of 94 degrees occurs. This conformation places the absolutely conserved Lys517 in a position to form electrostatic interactions with both ligands. The AMP is bound with the phosphate moiety interacting with Lys517 and the hydroxyl groups of the ribose forming hydrogen bonds with Asp413. The phenylalanine substrate binds in a hydrophobic pocket with the carboxylate group interacting with Lys517 and the alpha-amino group with Asp235. The structure reveals the role of the invariant residues within the superfamily of adenylate-forming enzymes and indicates a conserved mechanism of nucleotide binding and substrate activation.

Selected figure(s)

Figure 2.
Figure 2 Stereo diagram of the large N-terminal domain of PheA showing the bound ligands coloured as in Figure 1. The -sheet A is on the left-hand side, -sheet B is on the right-hand side, and the -barrel is at the top of the figure. The N-terminus of the protein is at the top of the figure. The disordered loop (residues 192 -196) near the active site is coloured violet.

Figure 6.
Figure 6 Schematic representation of the hydrogen bonding between PheA and the phenylalanine and AMP ligands.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Embo J (1997, 16, 4174-4183) copyright 1997.

Figures were selected by an automated process.