3IQE | pdb_00003iqe

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin and coenzyme F420

• PDB DOI: https://doi.org/10.2210/pdb3IQE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanopyrus kandleri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-20 Released: 2009-10-06 
• Deposition Author(s): Ceh, K.E., Demmer, U., Warkentin, E., Moll, J., Thauer, R.K., Shima, S., Ermler, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.228 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structural basis of the hydride transfer mechanism in F(420)-dependent methylenetetrahydromethanopterin dehydrogenase

Ceh, K., Demmer, U., Warkentin, E., Moll, J., Thauer, R.K., Shima, S., Ermler, U.

(2009) Biochemistry 48: 10098-10105

• PubMed: 19761261 
• DOI: https://doi.org/10.1021/bi901104d
• Primary Citation Related Structures: 
  3IQE, 3IQF, 3IQZ


• PubMed Abstract: 
  

  F(420)-dependent methylenetetrahydromethanopterin (methylene-H(4)MPT) dehydrogenase (Mtd) of Methanopyrus kandleri is an enzyme of the methanogenic energy metabolism that catalyzes the reversible hydride transfer between methenyl-H(4)MPT(+) and methylene-H(4)MPT using coenzyme F(420) as hydride carrier. We determined the structures of the Mtd-methylene-H(4)MPT, Mtd-methenyl-H(4)MPT(+), and the Mtd-methenyl-H(4)MPT(+)-F(420)H(2) complexes at 2.1, 2.0, and 1.8 A resolution, respectively. The pterin-imidazolidine-phenyl ring system is present in a new extended but not planar conformation which is virtually identical in methenyl-H(4)MPT(+) and methylene-H(4)MPT at the current resolution. Both substrates methenyl-H(4)MPT(+) and F(420)H(2) bind in a face to face arrangement to an active site cleft, thereby ensuring a direct hydride transfer between their C14a and C5 atoms, respectively. The polypeptide scaffold does not reveal any significant conformational change upon binding of the bulky substrates but in turn changes the conformations of the substrate rings either to avoid clashes between certain ring atoms or to adjust the rings involved in hydride transfer for providing an optimal catalytic efficiency.

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Organizational Affiliation: 
• Max-Planck-Institut fur Biophysik, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 198.1 kDa 
• Atom Count: 14,210 
• Modeled Residue Count: 1,692 
• Deposited Residue Count: 1,698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-dependent methylenetetrahydromethanopterin dehydrogenase	A, B, C, D, E, F	283	Methanopyrus kandleri	Mutation(s): 0  Gene Names: mtd EC: 1.5.99.9 (PDB Primary Data), 1.5.98.1 (UniProt)
UniProt
Find proteins for P94951 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)) Explore P94951  Go to UniProtKB:  P94951

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H4M	G [auth A], I [auth B], M [auth C], Q [auth D], U [auth E], X [auth F]	5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN C31 H45 N6 O16 P GBMIGEWJAPFSQI-UQXKJNEMSA-N
F42	H [auth A], J [auth B], N [auth C], R [auth D], V [auth E], Y [auth F]	COENZYME F420 C29 H36 N5 O18 P GEHSZWRGPHDXJO-NALJQGANSA-N
CA	K [auth B], L [auth B], O [auth C], S [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	P [auth C], T [auth D], W [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.228 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.148	α = 90
b = 165.539	β = 99.14
c = 93.552	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Ceh, K.E., Demmer, U., Warkentin, E., Moll, J., Thauer, R.K., Shima, S., Ermler, U.

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description