5YVS

Crystal Structure of the archaeal halo-thermophilic Red Sea brine pool alcohol dehydrogenase ADH/D1 bound to NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Identification and Experimental Characterization of an Extremophilic Brine Pool Alcohol Dehydrogenase from Single Amplified Genomes

Groetzinger, S.W.Karan, R.Strillinger, E.Bader, S.Frank, A.Al Rowaihi, I.S.Akal, A.Wackerow, W.Archer, J.A.Rueping, M.Weuster-Botz, D.Groll, M.Eppinger, J.Arold, S.T.

(2018) ACS Chem Biol 13: 161-170

  • DOI: https://doi.org/10.1021/acschembio.7b00792
  • Primary Citation of Related Structures:  
    5YVM, 5YVR, 5YVS

  • PubMed Abstract: 

    Because only 0.01% of prokaryotic genospecies can be cultured and in situ observations are often impracticable, culture-independent methods are required to understand microbial life and harness potential applications of microbes. Here, we report a methodology for the production of proteins with desired functions based on single amplified genomes (SAGs) from unculturable species. We use this method to resurrect an alcohol dehydrogenase (ADH/D1) from an uncharacterized halo-thermophilic archaeon collected from a brine pool at the bottom of the Red Sea. Our crystal structure of 5,6-dihydroxy NADPH-bound ADH/D1 combined with biochemical analyses reveal the molecular features of its halo-thermophily, its unique habitat adaptations, and its possible reaction mechanism for atypical oxygen activation. Our strategy offers a general guide for using SAGs as a source for scientific and industrial investigations of "microbial dark matter."


  • Organizational Affiliation

    King Abdullah University of Science and Technology , Biological and Environmental Science and Engineering Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
alcohol dehydrogenase409candidate division MSBL1 archaeon SCGC-AAA259E19Mutation(s): 0 
Gene Names: AKJ65_00115
UniProt
Find proteins for A0A133UP32 (candidate division MSBL1 archaeon SCGC-AAA259E19)
Explore A0A133UP32 
Go to UniProtKB:  A0A133UP32
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A133UP32
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
C [auth A]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.92α = 90
b = 104.84β = 90
c = 129.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
King Abdullah University of Science and Technology (KAUST)Saudi ArabiaURF/1/1976-06

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2018-02-07
    Changes: Database references, Structure summary
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references