PDBsum entry 3c3e

Transferase

PDB id: 3c3e

Contents

Protein chains

305 a.a. *

Ligands

FO1 ×4

GDP ×4

Waters ×38

* Residue conservation analysis

PDB id:

3c3e

Name:

Transferase

Title:

Crystal structure of 2-phospho-(s)-lactate transferase from methanosarcina mazei in complex with fo and gdp. Northeast structural genomics consortium target mar46

Structure:

2-phospho-l-lactate transferase. Chain: a, b, c, d. Synonym: lppg:fo, 2-phospho-(s)-lactate transferase. Engineered: yes

Source:

Methanosarcina mazei go1. Organism_taxid: 192952. Strain: go1 / dsm 3647 / goe1 / jcm 11883 / ocm 88. Atcc: baa-159. Gene: cofd, mm_1874. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.00Å R-factor: 0.206 R-free: 0.237

Authors:

F.Forouhar,M.Abashidze,H.Xu,L.L.Grochowski,J.Seetharaman,M.Hussain, A.P.Kuzin,Y.Chen,W.Zhou,R.Xiao,T.B.Acton,G.T.Montelione,A.Galinier, R.H.White,L.Tong,Northeast Structural Genomics Consortium (Nesg)

Key ref:

F.Forouhar et al. (2008). Molecular insights into the biosynthesis of the F420 coenzyme. J Biol Chem, 283, 11832-11840. PubMed id: 18252724 DOI: 10.1074/jbc.M710352200

Date:

28-Jan-08 Release date: 19-Feb-08

Protein chains

Q8PVT6  (COFD_METMA) -  2-phospho-L-lactate transferase from Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)

Seq: 303 a.a.

Struc: 305 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.8.28 - 2-phospho-L-lactate transferase.
• Reaction:
  1. (2S)-lactyl-2-diphospho-5'-guanosine + 7,8-didemethyl-8-hydroxy-5- deazariboflavin = oxidized coenzyme F420-0 + GMP + H⁺
  2. enolpyruvoyl-2-diphospho-5'-guanosine + 7,8-didemethyl-8-hydroxy-5- deazariboflavin = dehydro coenzyme F420-0 + GMP + H⁺
  3. 3-[(R)-glyceryl]-diphospho-5'-guanosine + 7,8-didemethyl-8-hydroxy-5- deazariboflavin = oxidized 3PG-factor420-0 + GMP + H⁺

(2S)-lactyl-2-diphospho-5'-guanosine + 7,8-didemethyl-8-hydroxy-5- deazariboflavin = oxidized coenzyme F420-0 (Bound ligand (Het Group name = GDP) matches with 85.71% similarity) + GMP + H(+)

enolpyruvoyl-2-diphospho-5'-guanosine + 7,8-didemethyl-8-hydroxy-5- deazariboflavin = dehydro coenzyme F420-0 + GMP (Bound ligand (Het Group name = GDP) matches with 85.71% similarity) + H(+)

3-[(R)-glyceryl]-diphospho-5'-guanosine + 7,8-didemethyl-8-hydroxy-5- deazariboflavin = oxidized 3PG-factor420-0 (Bound ligand (Het Group name = GDP) matches with 85.71% similarity) + GMP + H(+)

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

reference

DOI no: 10.1074/jbc.M710352200

J Biol Chem 283:11832-11840 (2008)

PubMed id: 18252724

Molecular insights into the biosynthesis of the F420 coenzyme.

F.Forouhar, M.Abashidze, H.Xu, L.L.Grochowski, J.Seetharaman, M.Hussain, A.Kuzin, Y.Chen, W.Zhou, R.Xiao, T.B.Acton, G.T.Montelione, A.Galinier, R.H.White, L.Tong.

ABSTRACT

Coenzyme F(420), a hydride carrier, is found in Archaea and some bacteria and has crucial roles in methanogenesis, antibiotic biosynthesis, DNA repair, and activation of antitubercular compounds. CofD, 2-phospho-l-lactate transferase, catalyzes the last step in the biosynthesis of F(420)-0 (F(420) without polyglutamate), by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (Fo). CofD is highly conserved among F(420)-producing organisms, and weak sequence homologs are also found in non-F(420)-producing organisms. This superfamily does not share any recognizable sequence conservation with other proteins. Here we report the first crystal structures of CofD, the free enzyme and two ternary complexes, with Fo and P(i) or with Fo and GDP, from Methanosarcina mazei. The active site is located at the C-terminal end of a Rossmann fold core, and three large insertions make significant contributions to the active site and dimer formation. The observed binding modes of Fo and GDP can explain known biochemical properties of CofD and are also supported by our binding assays. The structures provide significant molecular insights into the biosynthesis of the F(420) coenzyme. Large structural differences in the active site region of the non-F(420)-producing CofD homologs suggest that they catalyze a different biochemical reaction.

Selected figure(s)

Figure 3.
FIGURE 3. Binding mode of GDP. A, final 2F[o] - F[c] electron density for GDP molecule, contoured at 1 . Produced with PyMol (41). B, schematic drawing of the interactions between GDP and CofD. C, overlay of the structure of the ternary complex with Fo and GDP (in purple) and that with Fo and P[i] (in yellow). The P[i] is located about 1 Å from the -phosphate of GDP, but there is a large difference in the conformation of the glycine-rich loop, indicated with the red star.

Figure 4.
FIGURE 4. Binding mode of Fo. A, final 2F[o] - F[c] electron density for Fo, contoured at 1 . Produced with PyMol (41). B, schematic drawing of the interactions between Fo and CofD.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 11832-11840) copyright 2008.

Figures were selected by an automated process.