5TMA

Zymomonas mobilis pyruvate decarboxylase mutant PDC-2.3

PDB DOI: https://doi.org/10.2210/pdb5TMA/pdb

Classification: CELL ADHESION
Organism(s): Zymomonas mobilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-10-12 Released: 2017-10-18
Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.203
R-Value Work: 0.170
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme.

Sammond, D.W., Kastelowitz, N., Donohoe, B.S., Alahuhta, M., Lunin, V.V., Chung, D., Sarai, N.S., Yin, H., Mittal, A., Himmel, M.E., Guss, A.M., Bomble, Y.J.

(2018) Biotechnol Biofuels 11: 189-189

PubMed: 30002729 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s13068-018-1178-9
Primary Citation of Related Structures:
5TMA

PubMed Abstract:
Strategies for maximizing the microbial production of bio-based chemicals and fuels include eliminating branched points to streamline metabolic pathways. While this is often achieved by removing key enzymes, the introduction of nonnative enzymes can provide metabolic shortcuts, bypassing branched points to decrease the production of undesired side-products. Pyruvate decarboxylase (PDC) can provide such a shortcut in industrially promising thermophilic organisms; yet to date, this enzyme has not been found in any thermophilic organism. Incorporating nonnative enzymes into host organisms can be challenging in cases such as this, where the enzyme has evolved in a very different environment from that of the host.

Organizational Affiliation

1Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA.

Macromolecule Content

Total Structure Weight: 128.43 kDa
Atom Count: 10,255
Modelled Residue Count: 1,128
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate decarboxylase	A, B	576	Zymomonas mobilis	Mutation(s): 16 Gene Names: pdc, ZMO1360 EC: 4.1.1.1
UniProt
Find proteins for P06672 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)) Explore P06672 Go to UniProtKB: P06672
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06672
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP Query on TPP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain T [auth B] MOL2 format, chain C [auth A] MOL2 format, chain T [auth B]	C [auth A], T [auth B]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain T [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] E [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A]	FA [auth B] GA [auth B] HA [auth B] IA [auth B] JA [auth B] FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain U [auth B] MOL2 format, chain D [auth A] MOL2 format, chain U [auth B]	D [auth A], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.203
R-Value Work: 0.170
R-Value Observed: 0.172
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.44	α = 90
b = 124.44	β = 90
c = 173.825	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
Coot	model building
PROTEUM PLUS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-10-18

Deposition Author(s):

Alahuhta, P.M.

Lunin, V.V.

Revision History (Full details and data files)

Version 1.0: 2017-10-18
Type: Initial release
Version 1.1: 2019-06-05
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description