PDBsum entry 5tdf

Transferase

PDB id: 5tdf

Contents

Protein chains

421 a.a.

324 a.a.

Ligands

7A3

ADP

GOL ×6

ADE

Metals

_MG ×2

Waters ×821

PDB id:

5tdf

Name:

Transferase

Title:

Tev cleaved human atp citrate lyase bound to 4s hydroxycitrate

Structure:

Atp-citrate synthase. Chain: a. Fragment: unp residues 1-425. Synonym: atp-citrate (pro-s-)-lyase,acl,citrate cleavage enzyme. Engineered: yes. Atp-citrate synthase. Chain: b. Fragment: unp residues 488-810. Synonym: atp-citrate (pro-s-)-lyase,acl,citrate cleavage enzyme.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: acly. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Resolution:

1.80Å R-factor: 0.152 R-free: 0.191

Authors:

J.Hu,M.E.Fraser

Key ref:

J.Hu et al. (2017). Binding of hydroxycitrate to human ATP-citrate lyase. Acta Crystallogr D Struct Biol, 73, 660-671. PubMed id: 28777081 DOI: 10.1107/S2059798317009871

Date:

19-Sep-16 Release date: 09-Aug-17

Protein chain

P53396  (ACLY_HUMAN) -  ATP-citrate synthase from Homo sapiens

Seq: 1101 a.a.

Struc: 421 a.a.*

Protein chain

P53396  (ACLY_HUMAN) -  ATP-citrate synthase from Homo sapiens

Seq: 1101 a.a.

Struc: 324 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.2.3.3.8 - Atp citrate synthase.
• Reaction: oxaloacetate + acetyl-CoA + ADP + phosphate = citrate + ATP + CoA

oxaloacetate + acetyl-CoA + ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate = citrate (Bound ligand (Het Group name = 7A3) matches with 92.86% similarity) + ATP + CoA

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

reference

DOI no: 10.1107/S2059798317009871

Acta Crystallogr D Struct Biol 73:660-671 (2017)

PubMed id: 28777081

Binding of hydroxycitrate to human ATP-citrate lyase.

J.Hu, A.Komakula, M.E.Fraser.

ABSTRACT

Hydroxycitrate from the fruit of Garcinia cambogia [i.e. (2S,3S)-2-hydroxycitrate] is the best-known inhibitor of ATP-citrate lyase. Well diffracting crystals showing how the inhibitor binds to human ATP-citrate lyase were grown by modifying the protein. The protein was modified by introducing cleavage sites for Tobacco etch virus protease on either side of a disordered linker. The protein crystallized consisted of residues 2-425-ENLYFQ and S-488-810 of human ATP-citrate lyase. (2S,3S)-2-Hydroxycitrate binds in the same orientation as citrate, but the citrate-binding domain (residues 248-421) adopts a different orientation with respect to the rest of the protein (residues 4-247, 490-746 and 748-809) from that previously seen. For the first time, electron density was evident for the loop that contains His760, which is phosphorylated as part of the catalytic mechanism. The pro-S carboxylate of (2S,3S)-2-hydroxycitrate is available to accept a phosphoryl group from His760. However, when co-crystals were grown with ATP and magnesium ions as well as either the inhibitor or citrate, Mg²⁺-ADP was bound and His760 was phosphorylated. The phosphoryl group was not transferred to the organic acid. This led to the interpretation that the active site is trapped in an open conformation. The strategy of designing cleavage sites to remove disordered residues could be useful in determining the crystal structures of other proteins.