2FHJ

Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

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Literature

The structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes

Acharya, P.Warkentin, E.Ermler, U.Thauer, R.K.Shima, S.

(2006) J Mol Biol 357: 870-879

  • DOI: 10.1016/j.jmb.2006.01.015
  • Primary Citation of Related Structures:  
    2FHJ, 2FHK

  • PubMed Abstract: 
  • Formylmethanofuran:tetrahydromethanopterin formyltransferase is an essential enzyme in the one-carbon metabolism of methanogenic and sulfate-reducing archaea and of methylotrophic bacteria. The enzyme, which is devoid of a prosthetic group, catalyzes the reversible formyl transfer between the two substrates coenzyme methanofuran and coenzyme tetrahydromethanopterin (H4MPT) in a ternary complex catalytic mechanism ...

    Formylmethanofuran:tetrahydromethanopterin formyltransferase is an essential enzyme in the one-carbon metabolism of methanogenic and sulfate-reducing archaea and of methylotrophic bacteria. The enzyme, which is devoid of a prosthetic group, catalyzes the reversible formyl transfer between the two substrates coenzyme methanofuran and coenzyme tetrahydromethanopterin (H4MPT) in a ternary complex catalytic mechanism. The structure of the formyltransferase without its coenzymes has been determined earlier. We report here the structure of the enzyme in complex with both coenzymes at a resolution of 2.0 A. Methanofuran, characterized for the first time in an enzyme structure, is embedded in an elongated cleft at the homodimer interface and fixed by multiple hydrophobic interactions. In contrast, tetrahydromethanopterin is only weakly bound in a shallow and wide cleft that provides two binding sites. It is assumed that the binding of the bulky coenzymes induces conformational changes of the polypeptide in the range of 3A that close the H4MPT binding cleft and position the reactive groups of both substrates optimally for the reaction. The key residue for substrate binding and catalysis is the strictly conserved Glu245. Glu245, embedded in a hydrophobic region and completely buried upon tetrahydromethanopterin binding, is presumably protonated prior to the reaction and is thus able to stabilize the tetrahedral oxyanion intermediate generated by the nucleophilic attack of the N5 atom of tetrahydromethanopterin onto the formyl carbon atom of formylmethanofuran.


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Formylmethanofuran--tetrahydromethanopterin formyltransferaseA, B, C296Methanopyrus kandleriMutation(s): 0 
Gene Names: ftr
EC: 2.3.1.101
UniProt
Find proteins for Q49610 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938))
Explore Q49610 
Go to UniProtKB:  Q49610
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ49610
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Formylmethanofuran--tetrahydromethanopterin formyltransferaseD296Methanopyrus kandleriMutation(s): 1 
Gene Names: ftr
EC: 2.3.1.101
UniProt
Find proteins for Q49610 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938))
Explore Q49610 
Go to UniProtKB:  Q49610
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ49610
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H4Z
Query on H4Z

Download Ideal Coordinates CCD File 
K [auth A],
W [auth C]
5-(4-{[1-(2-AMINO-5-FORMYL-7-METHYL-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL)ETHYL]AMINO}PHENYL)-5-DEOXY-1-O-{5-O-[(1,3-DICARBOXYPROPOXY)(HYDROXY)PHOSPHORYL]PENTOFURANOSYL}PENTITOL
C31 H45 N6 O17 P
RMPHWTMYCVTPKB-BKULHTCLSA-N
 Ligand Interaction
MFN
Query on MFN

Download Ideal Coordinates CCD File 
CA [auth D],
I [auth A],
J [auth A],
V [auth C]
N-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL-N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}-D-GLUTAMINE
C35 H44 N4 O16
RGBIJPWAWLXPOC-XRVZLLLRSA-N
 Ligand Interaction
PE3
Query on PE3

Download Ideal Coordinates CCD File 
X [auth C]3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
C28 H58 O15
ILLKMACMBHTSHP-UHFFFAOYSA-N
 Ligand Interaction
PE4
Query on PE4

Download Ideal Coordinates CCD File 
DA [auth D],
EA [auth D],
L [auth A]
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth D],
E [auth A],
F [auth A],
G [auth A],
AA [auth D],
BA [auth D],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
Y [auth D],
Z [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
D L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85α = 90
b = 74.15β = 113.54
c = 103.87γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
XSCALEdata scaling
EPMRphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance