1M5H

Formylmethanofuran:tetrahydromethanopterin formyltransferase from Archaeoglobus fulgidus

PDB DOI: https://doi.org/10.2210/pdb1M5H/pdb

Classification: TRANSFERASE
Organism(s): Archaeoglobus fulgidus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2002-07-09 Released: 2002-07-26
Deposition Author(s): Mamat, B., Roth, A., Grimm, C., Ermler, U., Tziatzios, C., Schubert, D., Thauer, R.K., Shima, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.282
R-Value Work: 0.229
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

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

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

(2002) Protein Sci 11: 2168-2178

PubMed: 12192072 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1110/ps.0211002
Primary Citation of Related Structures:
1M5H, 1M5S

PubMed 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.

Organizational Affiliation:

Max-Planck-Institut für Biophysik, D-60528 Frankfurt am Main, Germany Institut für Biophysik der Johann Wolfgang Goethe-Universität, D-60590 Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 254.56 kDa
Atom Count: 19,658
Modelled Residue Count: 2,376
Deposited Residue Count: 2,376
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formylmethanofuran--tetrahydromethanopterin formyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H	297	Archaeoglobus fulgidus	Mutation(s): 0 EC: 2.3.1.101
UniProt
Find proteins for O28076 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28076 Go to UniProtKB: O28076
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O28076
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain CA [auth G] SDF format, chain DA [auth H] SDF format, chain EA [auth H] SDF format, chain FA [auth H] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain X [auth F] SDF format, chain Y [auth F] SDF format, chain Z [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain EA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F]	AA [auth G] BA [auth G] CA [auth G] DA [auth H] EA [auth H] AA [auth G], BA [auth G], CA [auth G], DA [auth H], EA [auth H], FA [auth H], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth C], P [auth C], Q [auth C], R [auth D], S [auth D], T [auth D], U [auth E], V [auth E], W [auth E], X [auth F], Y [auth F], Z [auth F]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Ligand Interaction