4JKI

Crystal Structure of N10-Formyltetrahydrofolate Synthetase with ZD9331, Formylphosphate, and ADP

Replaces:  3SIN

Summary for 4JKI

• Entry DOI: 10.2210/pdb4jki/pdb
• Related: 3PZX 3RBO 3SIN 4JIM 4JJK 4JJZ
• Descriptor: Formate--tetrahydrofolate ligase, 2,7-dimethyl-6-[(prop-1-yn-1-ylamino)methyl]quinazolin-4(3H)-one, formyl phosphate, ... (6 entities in total)
• Functional Keywords: ligase, ligase-ligase inhibitor complex, ligase/ligase inhibitor
• Biological source: Moorella thermoacetica
• Total number of polymer chains: 2
• Total formula weight: 121202.71

Authors

Celeste, L.R.,Lovelace, L.L.,Lebioda, L. (deposition date: 2013-03-09, release date: 2013-03-20, Last modification date: 2023-09-20)

Primary citation

Celeste, L.R.,Chai, G.,Bielak, M.,Minor, W.,Lovelace, L.L.,Lebioda, L.
Mechanism of N10-formyltetrahydrofolate synthetase derived from complexes with intermediates and inhibitors.
Protein Sci., 21:219-228, 2012

PubMed Abstract: N(10) -formyltetrahydrofolate synthetase (FTHFS) is a folate enzyme that catalyzes the formylation of tetrahydrofolate (THF) in an ATP dependent manner. Structures of FTHFS from the thermophilic homoacetogen, Moorella thermoacetica, complexed with (1) a catalytic intermediate-formylphosphate (XPO) and product-ADP; (2) with an inhibitory substrate analog-folate; (3) with XPO and an inhibitory THF analog, ZD9331, were used to analyze the enzyme mechanism. Nucleophilic attack of the formate ion on the gamma phosphate of ATP leads to the formation of XPO and the first product ADP. A channel that leads to the putative formate binding pocket allows for the binding of ATP and formate in random order. Formate binding is due to interactions with the gamma-phosphate moiety of ATP and additionally to two hydrogen bonds from the backbone nitrogen of Ala276 and the side chain of Arg97. Upon ADP dissociation, XPO reorients and moves to the position previously occupied by the beta-phosphate of ATP. Conformational changes that occur due to the XPO presence apparently allow for the recruitment of the third substrate, THF, with its pterin moiety positioned between Phe384 and Trp412. This position overlaps with that of the bound nucleoside, which is consistent with a catalytic mechanism hypothesis that FTHFS works via a sequential ping-pong mechanism. More specifically, a random bi uni uni bi ping-pong ter ter mechanism is proposed. Additionally, the native structure originally reported at a 2.5 Å resolution was redetermined at a 2.2 Å resolution.

PubMed: 22109967
DOI: 10.1002/pro.2005

Experimental method

X-RAY DIFFRACTION (2.6 Å)