PDBsum entry 3eu5

Transferase

PDB id: 3eu5

Contents

Protein chains

315 a.a. *

401 a.a. *

Ligands

GBO

Metals

_ZN

Waters ×132

* Residue conservation analysis

PDB id:

3eu5

Name:

Transferase

Title:

Crystal structure of ftase(alpha-subunit; beta-subunit delta c10) in complex with biotingpp

Structure:

Protein farnesyltransferase/geranylgeranyltransferase type- 1 subunit alpha. Chain: a. Synonym: caax farnesyltransferase subunit alpha, ras proteins prenyltransferase alpha, ftase-alpha, type i protein geranyl- geranyltransferase subunit alpha, ggtase-i-alpha. Engineered: yes. Protein farnesyltransferase subunit beta. Chain: b.

Source:

Rattus norvegicus. Rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.155 R-free: 0.207

Authors:

Z.Guo,U.T.T.Nguyen,C.Delon,R.S.Bon,W.Blankenfeldt,R.S.Goody, H.Waldmann,D.Wolters,K.Alexandrov

Key ref:

U.T.Nguyen et al. (2009). Analysis of the eukaryotic prenylome by isoprenoid affinity tagging. Nat Chem Biol, 5, 227-235. PubMed id: 19219049 DOI: 10.1038/nchembio.149

Date:

09-Oct-08 Release date: 07-Jul-09

Protein chain

Q04631  (FNTA_RAT) -  Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha from Rattus norvegicus

Seq: 377 a.a.

Struc: 315 a.a.

Protein chain

Q02293  (FNTB_RAT) -  Protein farnesyltransferase subunit beta from Rattus norvegicus

Seq: 437 a.a.

Struc: 401 a.a.

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 = GBO) matches with 47.50% 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 = GBO) matches with 42.22% 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: 10.1038/nchembio.149

Nat Chem Biol 5:227-235 (2009)

PubMed id: 19219049

Analysis of the eukaryotic prenylome by isoprenoid affinity tagging.

U.T.Nguyen, Z.Guo, C.Delon, Y.Wu, C.Deraeve, B.Fränzel, R.S.Bon, W.Blankenfeldt, R.S.Goody, H.Waldmann, D.Wolters, K.Alexandrov.

ABSTRACT

Protein prenylation is a widespread phenomenon in eukaryotic cells that affects many important signaling molecules. We describe the structure-guided design of engineered protein prenyltransferases and their universal synthetic substrate, biotin-geranylpyrophosphate. These new tools allowed us to detect femtomolar amounts of prenylatable proteins in cells and organs and to identify their cognate protein prenyltransferases. Using this approach, we analyzed the in vivo effects of protein prenyltransferase inhibitors. Whereas some of the inhibitors displayed the expected activities, others lacked in vivo activity or targeted a broader spectrum of prenyltransferases than previously believed. To quantitate the in vivo effect of the prenylation inhibitors, we profiled biotin-geranyl-tagged RabGTPases across the proteome by mass spectrometry. We also demonstrate that sites of active vesicular transport carry most of the RabGTPases. This approach enables a quantitative proteome-wide analysis of the regulation of protein prenylation and its modulation by therapeutic agents.

Selected figure(s)

Figure 1.
(a,b) Schematic representation of the reaction catalyzed by the two CAAX prenyltransferases FTase and GGTase-I (a) or RabGGTase in concert with REP (Rab escort protein) (b). The enzymes catalyze the formation of a thioether linkage between the prenyl group and one or two C-terminal cysteines of the protein substrate. (c) Chemical structure of BGPP in comparison with the natural substrates FPP and GGPP.

Figure 5.
(a) Western blot analysis of CFP-CAAX (CFP-TKCVIM) in vitro biotin-geranylated with FTase[W102T] (lanes 1 and 2), FTase[W102T_Y365F] (lanes 3 and 4) and FTase[W102T_Y154T] (lanes 5 and 6). (b) Optical slice through the active site of the BGPP-FTase[W102T_Y154T] complex superimposed with the structure of the BGPP–wild-type FTase complex. The picture is drawn as in Figure 4a, and the isoprenoid from the BGPP-FTase complex is shown in atomic colors while the BGPP in complex with the mutant is colored in blue. (c) Ball-and-stick representation of the active site of the wild-type FTase in complex with the FPP analog and peptide substrate superimposed with the BGPP from the BGPP-FTase[W102T_Y154T] complex. (d) Same as a but using RhoA as a substrate in combination with the wild-type enzyme or the GGTase-I[F53Y_Y126T] mutant.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2009, 5, 227-235) copyright 2009.

Figures were selected by an automated process.