2OUI | pdb_00002oui

D275P mutant of alcohol dehydrogenase from protozoa Entamoeba histolytica

PDB DOI: https://doi.org/10.2210/pdb2OUI/pdb

Classification: OXIDOREDUCTASE
Organism(s): Entamoeba histolytica
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-02-11 Released: 2008-02-12
Deposition Author(s): Frolow, F., Shimon, L., Burstein, Y., Goihberg, E., Peretz, M., Dym, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.178 (Depositor), 0.196 (DCC)
R-Value Work:
0.148 (Depositor)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Thermal stabilization of the protozoan Entamoeba histolytica alcohol dehydrogenase by a single proline substitution.

Goihberg, E., Dym, O., Tel-Or, S., Shimon, L., Frolow, F., Peretz, M., Burstein, Y.

(2008) Proteins 72: 711-719

PubMed: 18260103 Search on PubMed
DOI: https://doi.org/10.1002/prot.21946
Primary Citation Related Structures:
2NVB, 2OUI

PubMed Abstract:
Analysis of the three-dimensional structures of two closely related thermophilic and hyperthermophilic alcohol dehydrogenases (ADHs) from the respective microorganisms Entamoeba histolytica (EhADH1) and Thermoanaerobacter brockii (TbADH) suggested that a unique, strategically located proline residue (Pro275) at the center of the dimerization interface might be crucial for maintaining the thermal stability of TbADH. To assess the contribution of Pro275 to the thermal stability of the ADHs, we applied site-directed mutagenesis to replace Asp275 of EhADH1 with Pro (D275P-EhADH1) and conversely Pro275 of TbADH with Asp (P275D-TbADH). The results indicate that replacing Asp275 with Pro significantly enhances the thermal stability of EhADH1 (DeltaT(1/2)

Organizational Affiliation

Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.

Macromolecule Content

Total Structure Weight: 157.1 kDa
Atom Count: 12,226
Modeled Residue Count: 1,440
Deposited Residue Count: 1,440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADP-dependent alcohol dehydrogenase	A, B, C, D	360	Entamoeba histolytica	Mutation(s): 1 Gene Names: ADH1 EC: 1.1.1.2 (PDB Primary Data), 1.1.1.80 (UniProt)
UniProt
Find proteins for P35630 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore P35630 Go to UniProtKB: P35630
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35630
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain Y [auth C]	Y [auth C]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain Y [auth C] Interactions & Density Focus chain Y [auth C]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] MOL2 format, chain FA [auth D] mmCIF format, chain FA [auth D]	FA [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Interactions & Density Focus chain FA [auth D]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain Z [auth C] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain M [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain Z [auth C]	M [auth A], T [auth B], U [auth B], Z [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain Z [auth C] Interactions & Density Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain Z [auth C]
CAC Query on CAC Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain W [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain W [auth C]	CA [auth D], H [auth A], P [auth B], W [auth C]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain CA [auth D] Focus chain H [auth A] Focus chain P [auth B] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain H [auth A] Focus chain P [auth B] Focus chain W [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain E [auth A] SDF format, chain N [auth B] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain V [auth C]	AA [auth D], E [auth A], N [auth B], V [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain V [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain X [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain X [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain X [auth C]	EA [auth D] I [auth A] J [auth A] K [auth A] L [auth A] EA [auth D], I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], S [auth B], X [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Interactions & Density Focus chain EA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain O [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B]	BA [auth D], F [auth A], G [auth A], O [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain BA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] MOL2 format, chain DA [auth D] mmCIF format, chain DA [auth D]	DA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Interactions & Density Focus chain DA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.178 (Depositor), 0.196 (DCC)
R-Value Work: 0.148 (Depositor)
R-Value Observed: 0.150 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.921	α = 90
b = 144.104	β = 121.44
c = 80.073	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ProDC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-02-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-02-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2017-10-18
Changes: Refinement description
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-10-25
Changes: Data collection, Refinement description