4GKV

Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.008 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD.

Thomas, L.M.Harper, A.R.Miner, W.A.Ajufo, H.O.Branscum, K.M.Kao, L.Sims, P.A.

(2013) Acta Crystallogr.,Sect.F 69: 730-732

  • DOI: 10.1107/S1744309113015170

  • PubMed Abstract: 
  • The crystal structure of AdhP, a recombinantly expressed alcohol dehydrogenase from Escherichia coli K-12 (substrain MG1655), was determined to 2.01 Å resolution. The structure, which was solved using molecular replacement, also included the structur ...

    The crystal structure of AdhP, a recombinantly expressed alcohol dehydrogenase from Escherichia coli K-12 (substrain MG1655), was determined to 2.01 Å resolution. The structure, which was solved using molecular replacement, also included the structural and catalytic zinc ions and the cofactor nicotinamide adenine dinucleotide (NAD). The crystals belonged to space group P21, with unit-cell parameters a = 68.18, b = 118.92, c = 97.87 Å, β = 106.41°. The final R factor and Rfree were 0.138 and 0.184, respectively. The structure of the active site of AdhP suggested a number of residues that may participate in a proton relay, and the overall structure of AdhP, including the coordination to structural and active-site zinc ions, is similar to those of other tetrameric alcohol dehydrogenase enzymes.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019-5251, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alcohol dehydrogenase, propanol-preferring
A, B, C, D
336Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: adhP (yddN)
EC: 1.1.1.1
Find proteins for P39451 (Escherichia coli (strain K12))
Go to UniProtKB:  P39451
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
cleaved peptide fragment corresponding to the C-terminal His tag
P
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.008 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.160α = 90.00
b = 118.920β = 106.41
c = 97.870γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
CrystalCleardata collection
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references