5YVM

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

PDB DOI: https://doi.org/10.2210/pdb5YVM/pdb

Classification: OXIDOREDUCTASE
Organism(s): candidate division MSBL1 archaeon SCGC-AAA259E19
Expression System: Haloferax volcanii
Mutation(s): No

Deposited: 2017-11-26 Released: 2017-12-27
Deposition Author(s): Groetzinger, S.W., Strillinger, E., Frank, A., Eppinger, J., Groll, M., Arold, S.T.
Funding Organization(s): by King Abdullah University of Science and Technology (KAUST)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.223
R-Value Work: 0.172
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

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

PubMed: 29188989 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 45.2 kDa
Atom Count: 3,211
Modelled Residue Count: 403
Deposited Residue Count: 409
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alcohol dehydrogenase	A	409	candidate division MSBL1 archaeon SCGC-AAA259E19	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A133UP32
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NZQ Query on NZQ Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	5,6-DIHYDROXY-NADP C₂₁ H₃₂ N₇ O₁₉ P₃ LRAVAOPKUBJONV-IVCJQJMGSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.223
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.19	α = 90
b = 103.72	β = 90
c = 128.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MoRDa	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-12-27

Deposition Author(s):

Funding Organization	Location	Grant Number
by King Abdullah University of Science and Technology (KAUST)	Saudi Arabia	URF/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, Experimental preparation, Source and taxonomy, Structure summary
Version 1.2: 2018-02-07
Changes: Database references, Structure summary
Version 1.3: 2023-11-22
Changes: Data collection, Database references, Refinement description