Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 198.01 kDa 
• Atom Count: 13995 
• Modelled Residue Count: 1647 
• Deposited Residue Count: 1738 
• Unique protein chains: 1

4PAB

Crystal structure of the precursor form of rat DMGDH complexed with tetrahydrofolate

• PDB DOI: 10.2210/pdb4PAB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-04-07 Released: 2014-06-18 
• Deposition Author(s): Luka, Z., Pakhomova, S., Loukachevitch, L.V., Newcomer, M.E., Wagner, C.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.231 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Literature

Folate in demethylation: The crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate.

Luka, Z., Pakhomova, S., Loukachevitch, L.V., Newcomer, M.E., Wagner, C.

(2014) Biochem Biophys Res Commun 449: 392-398

• PubMed: 24858690 
• DOI: 10.1016/j.bbrc.2014.05.064
• Primary Citation of Related Structures:  
  4P9S, 4PAA, 4PAB


• PubMed Abstract: 
  

Dimethylglycine dehydrogenase (DMGDH) is a mammalian mitochondrial enzyme which plays an important role in the utilization of methyl groups derived from choline. DMGDH is a flavin containing enzyme which catalyzes the oxidative demethylation of dimethylglycine in vitro with the formation of sarcosine (N-methylglycine), hydrogen peroxide and formaldehyde. DMGDH binds tetrahydrofolate (THF) in vivo, which serves as an acceptor of formaldehyde and in the cell the product of the reaction is 5,10-methylenetetrahydrofolate instead of formaldehyde. To gain insight into the mechanism of the reaction we solved the crystal structures of the recombinant mature and precursor forms of rat DMGDH and DMGDH-THF complexes. Both forms of DMGDH reveal similar kinetic parameters and have the same tertiary structure fold with two domains formed by N- and C-terminal halves of the protein. The active center is located in the N-terminal domain while the THF binding site is located in the C-terminal domain about 40Å from the isoalloxazine ring of FAD. The folate binding site is connected with the enzyme active center via an intramolecular channel. This suggests the possible transfer of the intermediate imine of dimethylglycine from the active center to the bound THF where they could react producing a 5,10-methylenetetrahydrofolate. Based on the homology of the rat and human DMGDH the structural basis for the mechanism of inactivation of the human DMGDH by naturally occurring His109Arg mutation is proposed.

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Organizational Affiliation: 

Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dimethylglycine dehydrogenase	A, B	869	Rattus norvegicus	Mutation(s): 6  Gene Names: Dmgdh EC: 1.5.8.4
UniProt
Find proteins for Q63342 (Rattus norvegicus) Explore Q63342  Go to UniProtKB:  Q63342

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], I [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
THG	D [auth A], J [auth B]	(6S)-5,6,7,8-TETRAHYDROFOLATE C19 H23 N7 O6 MSTNYGQPCMXVAQ-RYUDHWBXSA-N
SCN	E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.231 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.182	α = 90
b = 107.215	β = 92.16
c = 114.466	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-04-07 
• Released Date: 2014-06-18 
Deposition Author(s): Luka, Z., Pakhomova, S., Loukachevitch, L.V., Newcomer, M.E., Wagner, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK15289

Revision History  

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2014-07-16
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Derived calculations
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence