PDBsum entry 4l9p

Transferase

PDB id: 4l9p

Contents

Protein chains

335 a.a.

452 a.a.

Ligands

LYS-CYS-VAL-VAL-MET

EDO ×9

FII

Metals

_CL ×3

_ZN

Waters ×778

PDB id:

4l9p

Name:

Transferase

Title:

Crystal structure of aspergillus fumigatus protein farnesyltransferase complexed with the fii analog, fpt-ii, and the kcvvm peptide

Structure:

Caax farnesyltransferase alpha subunit ram2. Chain: a. Engineered: yes. Mutation: yes. Caax farnesyltransferase beta subunit ram1. Chain: b. Engineered: yes. Lys-cys-val-val-met (caax peptide). Chain: c.

Source:

Aspergillus fumigatus. Organism_taxid: 330879. Strain: af293. Gene: afua_4g07800. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: afua_4g10330. Synthetic: yes

Resolution:

1.45Å R-factor: 0.126 R-free: 0.152

Authors:

M.F.Mabanglo,M.A.Hast,L.S.Beese

Key ref:

M.F.Mabanglo et al. (2014). Crystal structures of the fungal pathogen Aspergillus fumigatus protein farnesyltransferase complexed with substrates and inhibitors reveal features for antifungal drug design. Protein Sci, 23, 289-301. PubMed id: 24347326 DOI: 10.1002/pro.2411

Date:

18-Jun-13 Release date: 01-Jan-14

Protein chain

Q4WP27  (Q4WP27_ASPFU) -  Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha from Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)

Seq: 353 a.a.

Struc: 335 a.a.*

Protein chain

Q4WPS9  (Q4WPS9_ASPFU) -  Protein farnesyltransferase subunit beta from Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)

Seq: 519 a.a.

Struc: 452 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.2.5.1.58 - protein farnesyltransferase.
• Reaction: L-cysteinyl-[protein] + (2E,6E)-farnesyl diphosphate = S-(2E,6E)- farnesyl-L-cysteinyl-[protein] + diphosphate

L-cysteinyl-[protein] (Bound ligand (Het Group name = FII) matches with 50.00% similarity) + (2E,6E)-farnesyl diphosphate = S-(2E,6E)- farnesyl-L-cysteinyl-[protein] + diphosphate

• Cofactor: Mg(2+); Zn(2+)
• Enzyme class 2: Chain A: E.C.2.5.1.59 - protein geranylgeranyltransferase type I.
• Reaction: geranylgeranyl diphosphate + L-cysteinyl-[protein] = S-geranylgeranyl-L- cysteinyl-[protein] + diphosphate

geranylgeranyl diphosphate (Bound ligand (Het Group name = FII) matches with 43.24% similarity) + L-cysteinyl-[protein] = S-geranylgeranyl-L- cysteinyl-[protein] + diphosphate

• Cofactor: Zn(2+)

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/pro.2411

Protein Sci 23:289-301 (2014)

PubMed id: 24347326

Crystal structures of the fungal pathogen Aspergillus fumigatus protein farnesyltransferase complexed with substrates and inhibitors reveal features for antifungal drug design.

M.F.Mabanglo, M.A.Hast, N.B.Lubock, H.W.Hellinga, L.S.Beese.

ABSTRACT

Species of the fungal genus Aspergillus are significant human and agricultural pathogens that are often refractory to existing antifungal treatments. Protein farnesyltransferase (FTase), a critical enzyme in eukaryotes, is an attractive potential target for antifungal drug discovery. We report high-resolution structures of A. fumigatus FTase (AfFTase) in complex with substrates and inhibitors. Comparison of structures with farnesyldiphosphate (FPP) bound in the absence or presence of peptide substrate, corresponding to successive steps in ordered substrate binding, revealed that the second substrate-binding step is accompanied by motions of a loop in the catalytic site. Re-examination of other FTase structures showed that this motion is conserved. The substrate- and product-binding clefts in the AfFTase active site are wider than in human FTase (hFTase). Widening is a consequence of small shifts in the α-helices that comprise the majority of the FTase structure, which in turn arise from sequence variation in the hydrophobic core of the protein. These structural effects are key features that distinguish fungal FTases from hFTase. Their variation results in differences in steady-state enzyme kinetics and inhibitor interactions and presents opportunities for developing selective anti-fungal drugs by exploiting size differences in the active sites. We illustrate the latter by comparing the interaction of ED5 and Tipifarnib with hFTase and AfFTase. In AfFTase, the wider groove enables ED5 to bind in the presence of FPP, whereas in hFTase it binds only in the absence of substrate. Tipifarnib binds similarly to both enzymes but makes less extensive contacts in AfFTase with consequently weaker binding.