3IQF

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin

PDB DOI: https://doi.org/10.2210/pdb3IQF/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.200
R-Value Work: 0.160
R-Value Observed: 0.162

Starting Model: experimental
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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 Search on PubMed
DOI: https://doi.org/10.1021/bi901104d
Primary Citation of 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 386.75 kDa
Atom Count: 27,835
Modelled Residue Count: 3,384
Deposited Residue Count: 3,396
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-dependent methylenetetrahydromethanopterin dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P94951
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E4M Query on E4M Download Ideal Coordinates CCD File SDF format, chain BA [auth K] SDF format, chain EA [auth L] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain V [auth G] SDF format, chain W [auth H] SDF format, chain X [auth I] SDF format, chain Z [auth J] MOL2 format, chain BA [auth K] MOL2 format, chain EA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] MOL2 format, chain W [auth H] MOL2 format, chain X [auth I] MOL2 format, chain Z [auth J] mmCIF format, chain BA [auth K] mmCIF format, chain EA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain V [auth G] mmCIF format, chain W [auth H] mmCIF format, chain X [auth I] mmCIF format, chain Z [auth J]	BA [auth K] EA [auth L] M [auth A] N [auth B] P [auth C] BA [auth K], EA [auth L], M [auth A], N [auth B], P [auth C], Q [auth D], R [auth E], T [auth F], V [auth G], W [auth H], X [auth I], Z [auth J]	1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol C₃₁ H₄₄ N₆ O₁₆ P RANKJVUGLXUXOL-CAFBYHECSA-O		Interactions Focus chain BA [auth K] Focus chain EA [auth L] Focus chain M [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Z [auth J] Interactions & Density Focus chain BA [auth K] Focus chain EA [auth L] Focus chain M [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Z [auth J]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain CA [auth K] SDF format, chain DA [auth K] SDF format, chain FA [auth L] SDF format, chain O [auth B] SDF format, chain S [auth E] SDF format, chain Y [auth I] MOL2 format, chain AA [auth J] MOL2 format, chain CA [auth K] MOL2 format, chain DA [auth K] MOL2 format, chain FA [auth L] MOL2 format, chain O [auth B] MOL2 format, chain S [auth E] MOL2 format, chain Y [auth I] mmCIF format, chain AA [auth J] mmCIF format, chain CA [auth K] mmCIF format, chain DA [auth K] mmCIF format, chain FA [auth L] mmCIF format, chain O [auth B] mmCIF format, chain S [auth E] mmCIF format, chain Y [auth I]	AA [auth J] CA [auth K] DA [auth K] FA [auth L] O [auth B] AA [auth J], CA [auth K], DA [auth K], FA [auth L], O [auth B], S [auth E], Y [auth I]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Focus chain CA [auth K] Focus chain DA [auth K] Focus chain FA [auth L] Focus chain O [auth B] Focus chain S [auth E] Focus chain Y [auth I] Interactions & Density Focus chain AA [auth J] Focus chain CA [auth K] Focus chain DA [auth K] Focus chain FA [auth L] Focus chain O [auth B] Focus chain S [auth E] Focus chain Y [auth I]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain U [auth F] MOL2 format, chain U [auth F] mmCIF format, chain U [auth F]	U [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain U [auth F] Interactions & Density Focus chain U [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.200
R-Value Work: 0.160
R-Value Observed: 0.162
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.4	α = 90
b = 167.1	β = 113.6
c = 122.5	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-10-06

Deposition Author(s):

Revision History (Full details and data files)

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

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Help and Resources

3IQF

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)