PDBsum entry 2hs3

Ligase

PDB id: 2hs3

Contents

Protein chain

602 a.a. *

Ligands

PO4

FGR

Waters ×471

* Residue conservation analysis

PDB id:

2hs3

Name:

Ligase

Title:

T. Maritima purl complexed with fgar

Structure:

Phosphoribosylformylglycinamidine synthase ii. Chain: a. Synonym: purl. Formylglycinamide ribonucleotide amidotransferase. Fgam synthase ii. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Gene: purl. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.193 R-free: 0.250

Authors:

S.E.Ealick,M.Morar

Key ref:

M.Morar et al. (2006). Complexed structures of formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima describe a novel ATP binding protein superfamily. Biochemistry, 45, 14880-14895. PubMed id: 17154526 DOI: 10.1021/bi061591u

Date:

21-Jul-06 Release date: 09-Jan-07

Protein chain

Q9X0X3  (PURL_THEMA) -  Phosphoribosylformylglycinamidine synthase subunit PurL from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 603 a.a.

Struc: 602 a.a.

Enzyme reactions

• Enzyme class: E.C.6.3.5.3 - phosphoribosylformylglycinamidine synthase.
• Pathway: Purine Biosynthesis (early stages)
• Reaction: N₂-formyl-N₁-(5-phospho-beta-D-ribosyl)glycinamide + L-glutamine + ATP + H2O = 2-formamido-N₁-(5-O-phospho-beta-D-ribosyl)acetamidine + L-glutamate + ADP + phosphate + H⁺

N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + L-glutamine + ATP + H2O = 2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + L-glutamate (Bound ligand (Het Group name = FGR) matches with 62.07% similarity) + ADP + phosphate + H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

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

reference

DOI no: 10.1021/bi061591u

Biochemistry 45:14880-14895 (2006)

PubMed id: 17154526

Complexed structures of formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima describe a novel ATP binding protein superfamily.

M.Morar, R.Anand, A.A.Hoskins, J.Stubbe, S.E.Ealick.

ABSTRACT

Formylglycinamide ribonucleotide amidotransferase (FGAR-AT) catalyzes the ATP-dependent synthesis of formylglycinamidine ribonucleotide (FGAM) from formylglycinamide ribonucleotide (FGAR) and glutamine in the fourth step of the purine biosynthetic pathway. FGAR-AT is encoded by the purL gene. Two types of PurL have been detected. The first type, found in eukaryotes and Gram-negative bacteria, consists of a single 140 kDa polypeptide chain and is designated large PurL (lgPurL). The second type, small PurL (smPurL), is found in archaea and Gram-positive bacteria and consists of an 80 kDa polypeptide chain. SmPurL requires two additional gene products, PurQ and PurS, for activity. PurL is a member of a protein superfamily that contains a novel ATP-binding domain. Structures of several members of this superfamily are available in the unliganded form. We determined five different structures of FGAR-AT from Thermotoga maritima in the presence of substrates, a substrate analogue, and a product. These complexes have allowed a detailed description of the novel ATP-binding motif. The availability of a ternary complex enabled mapping of the active site, thus identifying potential residues involved in catalysis. The complexes show a conformational change in the active site compared to the unliganded structure. Surprising discoveries, an ATP molecule in an auxiliary site of the protein and the conformational changes associated with its binding, provoke speculation about the regulatory role of the auxiliary site in formation of the PurLSQ complex as well as the evolutionary relationship of PurLs from different organisms.