PDBsum entry 1m5h

Transferase

PDB id: 1m5h

Contents

Protein chains

(+ 2 more) 297 a.a. *

Metals

__K ×24

Waters ×1794

* Residue conservation analysis

PDB id:

1m5h

Name:

Transferase

Title:

Formylmethanofuran:tetrahydromethanopterin formyltransferase from archaeoglobus fulgidus

Structure:

Formylmethanofuran--tetrahydromethanopterin formyltransferase. Chain: a, b, c, d, e, f, g, h. Synonym: formylmethanofuran:tetrahydromethanopterin formyltransferase. Ftr-2. Ftr-2 af2207. Engineered: yes

Source:

Archaeoglobus fulgidus. Organism_taxid: 2234. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.00Å R-factor: 0.229 R-free: 0.282

Authors:

B.Mamat,A.Roth,C.Grimm,U.Ermler,C.Tziatzios,D.Schubert,R.K.Thauer, S.Shima

Key ref:

B.Mamat et al. (2002). Crystal structures and enzymatic properties of three formyltransferases from archaea: environmental adaptation and evolutionary relationship. Protein Sci, 11, 2168-2178. PubMed id: 12192072 DOI: 10.1110/ps.0211002

Date:

09-Jul-02 Release date: 26-Jul-02

Protein chains

O28076  (FTR_ARCFU) -  Formylmethanofuran--tetrahydromethanopterin formyltransferase from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)

Seq: 297 a.a.

Struc: 297 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.3.1.101 - formylmethanofuran--tetrahydromethanopterin N-formyltransferase.
• Pathway: Methane Biosynthesis
• Reaction: N-formylmethanofuran + 5,6,7,8-tetrahydromethanopterin + H⁺ = N₅- formyl-5,6,7,8-tetrahydromethanopterin + methanofuran

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

Added reference

DOI no: 10.1110/ps.0211002

Protein Sci 11:2168-2178 (2002)

PubMed id: 12192072

Crystal structures and enzymatic properties of three formyltransferases from archaea: environmental adaptation and evolutionary relationship.

B.Mamat, A.Roth, C.Grimm, U.Ermler, C.Tziatzios, D.Schubert, R.K.Thauer, S.Shima.

ABSTRACT

Formyltransferase catalyzes the reversible formation of formylmethanofuran from N(5)-formyltetrahydromethanopterin and methanofuran, a reaction involved in the C1 metabolism of methanogenic and sulfate-reducing archaea. The crystal structure of the homotetrameric enzyme from Methanopyrus kandleri (growth temperature optimum 98 degrees C) has recently been solved at 1.65 A resolution. We report here the crystal structures of the formyltransferase from Methanosarcina barkeri (growth temperature optimum 37 degrees C) and from Archaeoglobus fulgidus (growth temperature optimum 83 degrees C) at 1.9 A and 2.0 A resolution, respectively. Comparison of the structures of the three enzymes revealed very similar folds. The most striking difference found was the negative surface charge, which was -32 for the M. kandleri enzyme, only -8 for the M. barkeri enzyme, and -11 for the A. fulgidus enzyme. The hydrophobic surface fraction was 50% for the M. kandleri enzyme, 56% for the M. barkeri enzyme, and 57% for the A. fulgidus enzyme. These differences most likely reflect the adaptation of the enzyme to different cytoplasmic concentrations of potassium cyclic 2,3-diphosphoglycerate, which are very high in M. kandleri (>1 M) and relatively low in M. barkeri and A. fulgidus. Formyltransferase is in a monomer/dimer/tetramer equilibrium that is dependent on the salt concentration. Only the dimers and tetramers are active, and only the tetramers are thermostable. The enzyme from M. kandleri is a tetramer, which is active and thermostable only at high concentrations of potassium phosphate (>1 M) or potassium cyclic 2,3-diphosphoglycerate. Conversely, the enzyme from M. barkeri and A. fulgidus already showed these properties, activity and stability, at much lower concentrations of these strong salting-out salts.

Selected figure(s)

Figure 5.
Fig. 5. Structure of the formyltransferase. (A) The tetramer presented as a Ribbon diagram indicates a particularly extended contact region between subunits 1 (red) and 2 (green) and the equivalent subunits 3 (blue) and 4 (orange). (B) The Ribbon diagram of the monomer visualizes the location of the insertion region (blue), the meander region (black circle), and the loop between strands 6 and 7 (black arrow). (C) The stereo C[ ]-plot of the superimposed monomers of the enzymes from M. barkeri (red), A. fulgidus (yellow), and M. kandleri (green) documents their similar fold, in particular, in the core regions of the two lobes. This figure was generated using the program MOLSCRIPT (Kraulis 1991).

Figure 6.
Fig. 6. The electrostatic properties of the formyltransferase tetramer from (A) M. barkeri, (B) A. fulgidus, and (C) M. kandleri. The molecule surface is coated according to the electrostatic potential: The extreme ranges of red and blue represent potentials of -20k[B]T and 20k[B]T, respectively (where k[B] is the Boltzmann constant and T is temperature). The electrostatic surface potential of the enzymes from M. barkeri and A. fulgidus is nearly neutral, and that of the M. kandleri enzyme highly negative, reflecting the dominance of acidic to basic residues. The potentials are calculated under salt-free conditions. The figure was generated using the program GRASP (Nicholls et al. 1993).

The above figures are reprinted by permission from the Protein Society: Protein Sci (2002, 11, 2168-2178) copyright 2002.

Figures were selected by an automated process.