6TGE

NADP dependent methylene-tetrahydromethanopterin dehydrogenase-NADP+-methenyl-H4MPT+ complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase.

Huang, G.Wagner, T.Demmer, U.Warkentin, E.Ermler, U.Shima, S.

(2020) J Mol Biol 432: 2042-2054

  • DOI: 10.1016/j.jmb.2020.01.042
  • Primary Citation of Related Structures:  
    6TGE, 6TLK, 6TM3, 6YKA, 6YKB, 6YK9

  • PubMed Abstract: 
  • NADP-dependent methylene-tetrahydromethanopterin (methylene-H 4 MPT) dehydrogenase (MtdA) catalyzes the reversible dehydrogenation of methylene-H 4 MPT to form methenyl-H 4 MPT + by using NADP + as a hydride acceptor ...

    NADP-dependent methylene-tetrahydromethanopterin (methylene-H 4 MPT) dehydrogenase (MtdA) catalyzes the reversible dehydrogenation of methylene-H 4 MPT to form methenyl-H 4 MPT + by using NADP + as a hydride acceptor. This hydride transfer reaction is involved in the oxidative metabolism from formaldehyde to CO 2 in methylotrophic and methanotrophic bacteria. Here, we report on the crystal structures of the ternary MtdA-substrate complexes from Methylorubrum extorquens AM1 obtained in open and closed forms. Their conversion is accomplished by opening/closing the active site cleft via a 15° rotation of the NADP, relative to the pterin domain. The 1.08 Å structure of the closed and active enzyme-NADP-methylene-H 4 MPT complex allows a detailed geometric analysis of the bulky substrates and a precise prediction of the hydride trajectory. Upon domain closure, the bulky substrate rings become compressed resulting in a tilt of the imidazolidine group of methylene-H 4 MPT that optimizes the geometry for hydride transfer. An additional 1.5 Å structure of MtdA in complex with the nonreactive NADP + and methenyl-H 4 MPT + revealed an extremely short distance between nicotinamide-C4 and imidazoline-C14a of 2.5 Å, which demonstrates the strong pressure imposed. The pterin-imidazolidine-phenyl butterfly angle of methylene-H 4 MPT bound to MtdA is smaller than that in the enzyme-free state but is similar to that in H 2 - and F 420 -dependent methylene-H 4 MPT dehydrogenases. The concept of compression-driven hydride transfer including quantum mechanical hydrogen tunneling effects, which are established for flavin- and NADP-dependent enzymes, can be expanded to hydride-transferring H 4 MPT-dependent enzymes.


    Organizational Affiliation

    Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch Straße 10, 35043, Marburg, Germany. Electronic address: shima@mpi-marburg.mpg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional NADP-dependent methylenetetrahydromethanopterin dehydrogenase/methylenetetrahydrofolate dehydrogenase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
288Methylorubrum extorquensMutation(s): 0 
Gene Names: mtdABV511_24355TK0001_4179
EC: 1.5.1 (PDB Primary Data), 1.5.1.5 (UniProt)
UniProt
Find proteins for P55818 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1))
Explore P55818 
Go to UniProtKB:  P55818
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H4M (Subject of Investigation/LOI)
Query on H4M

Download Ideal Coordinates CCD File 
BB [auth M] , BC [auth X] , CA [auth B] , EA [auth C] , EB [auth N] , FA [auth D] , GB [auth O] , IB [auth P] , 
BB [auth M],  BC [auth X],  CA [auth B],  EA [auth C],  EB [auth N],  FA [auth D],  GB [auth O],  IB [auth P],  JA [auth E],  LA [auth F],  LB [auth Q],  NA [auth G],  NB [auth R],  PA [auth H],  PB [auth S],  SA [auth I],  SB [auth T],  UA [auth J],  UB [auth U],  WB [auth V],  XA [auth K],  Z [auth A],  ZA [auth L],  ZB [auth W]
5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN
C31 H45 N6 O16 P
GBMIGEWJAPFSQI-UQXKJNEMSA-N
 Ligand Interaction
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
AB [auth M] , AC [auth X] , BA [auth B] , DA [auth C] , DB [auth N] , FB [auth O] , GA [auth D] , HB [auth P] , 
AB [auth M],  AC [auth X],  BA [auth B],  DA [auth C],  DB [auth N],  FB [auth O],  GA [auth D],  HB [auth P],  IA [auth E],  KA [auth F],  KB [auth Q],  MA [auth G],  MB [auth R],  OA [auth H],  OB [auth S],  RA [auth I],  RB [auth T],  TA [auth J],  TB [auth U],  VB [auth V],  WA [auth K],  Y [auth A],  YA [auth L],  YB [auth W]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth A], CB [auth M], HA [auth D], JB [auth P], QA [auth H], QB [auth S], VA [auth J], XB [auth V]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.64α = 94.79
b = 123.5β = 100.39
c = 167.3γ = 108.97
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2019-11-15 
  • Released Date: 2020-02-26 
  • Deposition Author(s): Ermler, U., Shima, S.

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references