1MC5

Ternary complex of Human glutathione-dependent formaldehyde dehydrogenase with S-(hydroxymethyl)glutathione and NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Human glutathione-dependent formaldehyde dehydrogenase. Structural changes associated with Ternary Complex formation

Sanghani, P.C.Bosron, W.F.Hurley, T.D.

(2002) Biochemistry 41: 15189-15194


  • PubMed Abstract: 
  • Human glutathione-dependent formaldehyde dehydrogenase plays an important role in the metabolism of glutathione adducts such as S-(hydroxymethyl)glutathione and S-nitrosoglutathione. The role of specific active site residues in binding these physiolo ...

    Human glutathione-dependent formaldehyde dehydrogenase plays an important role in the metabolism of glutathione adducts such as S-(hydroxymethyl)glutathione and S-nitrosoglutathione. The role of specific active site residues in binding these physiologically important substrates and the structural changes during the catalytic cycle of glutathione-dependent formaldehyde dehydrogenase was examined by determining the crystal structure of a ternary complex with S-(hydroxymethyl)glutathione and the reduced coenzyme to 2.6 A resolution. The formation of the ternary complex caused the movement of the catalytic domain toward the coenzyme-binding domain. This represents the first observation of domain closure in glutathione-dependent formaldehyde dehydrogenase in response to substrate binding. A water molecule adjacent to the 2'-ribose hydroxyl of NADH suggests that the alcohol proton is relayed to solvent directly from the coenzyme, rather than through the action of the terminal histidine residue as observed in the proton relay system for class I alcohol dehydrogenases. S-(Hydroxymethyl)glutathione is directly coordinated to the active site zinc and forms interactions with the highly conserved residues Arg114, Asp55, Glu57, and Thr46. The active site zinc has a tetrahedral coordination environment with Cys44, His66, and Cys173 as the three protein ligands in addition to S-(hydroxymethyl)glutathione. This is in contrast to zinc coordination in the binary coenzyme complex where all of the ligands were contributed by the enzyme and included Glu67 as the fourth protein ligand. This change in zinc coordination is accomplished by an approximately 2.3 A movement of the catalytic zinc.


    Organizational Affiliation

    Center for Structural Biology, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alcohol dehydrogenase class III chi chain
A, B
374Homo sapiensGene Names: ADH5 (ADHX, FDH)
EC: 1.1.1.-, 1.1.1.1, 1.1.1.284
Find proteins for P11766 (Homo sapiens)
Go to Gene View: ADH5
Go to UniProtKB:  P11766
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

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A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
AHE
Query on AHE

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A
2-AMINO-4-[1-CARBOXYMETHYL-CARBAMOYL)-2-HYDROXYMETHYLSULFANYL-ETHYLCARBAMOYL]-BUTYRIC ACID
S-HYDROXYMETHYL GLUTATHIONE
C11 H19 N3 O7 S
PIUSLWSYOYFRFR-BQBZGAKWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.197 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.656α = 90.00
b = 78.656β = 90.00
c = 311.428γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance