5NPU | pdb_00005npu

Inferred ancestral pyruvate decarboxylase

PDB DOI: https://doi.org/10.2210/pdb5NPU/pdb

Classification: LYASE
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-04-19 Released: 2018-03-07
Deposition Author(s): Buddrus, L., Crennell, S.J., Leak, D.J., Danson, M.J., Andrews, E.S.V., Arcus, V.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.319 (Depositor), 0.324 (DCC)
R-Value Work:
0.246 (Depositor), 0.248 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of an inferred ancestral bacterial pyruvate decarboxylase.

Buddrus, L., Andrews, E.S.V., Leak, D.J., Danson, M.J., Arcus, V.L., Crennell, S.J.

(2018) Acta Crystallogr F Struct Biol Commun 74: 179-186

PubMed: 29497023 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X18002819
Primary Citation Related Structures:
5NPU

PubMed Abstract:
Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a key enzyme in homofermentative metabolism where ethanol is the major product. PDCs are thiamine pyrophosphate- and Mg ²⁺ ion-dependent enzymes that catalyse the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. As this enzyme class is rare in bacteria, current knowledge of bacterial PDCs is extremely limited. One approach to further the understanding of bacterial PDCs is to exploit the diversity provided by evolution. Ancestral sequence reconstruction (ASR) is a method of computational molecular evolution to infer extinct ancestral protein sequences, which can then be synthesized and experimentally characterized. Through ASR a novel PDC was generated, designated ANC27, that shares only 78% amino-acid sequence identity with its closest extant homologue (Komagataeibacter medellinensis PDC, GenBank accession No. WP_014105323.1), yet is fully functional. Crystals of this PDC diffracted to 3.5 Å resolution. The data were merged in space group P3 ₂21, with unit-cell parameters a = b = 108.33, c = 322.65 Å, and contained two dimers (two tetramer halves) in the asymmetric unit. The structure was solved by molecular replacement using PDB entry 2wvg as a model, and the final R values were R _work = 0.246 (0.3671 in the highest resolution bin) and R _free = 0.319 (0.4482 in the highest resolution bin). Comparison with extant bacterial PDCs supports the previously observed correlation between decreased tetramer interface area (and number of interactions) and decreased thermostability.

Organizational Affiliation

School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, England.

Macromolecule Content

Total Structure Weight: 244.71 kDa
Atom Count: 16,656
Modeled Residue Count: 2,182
Deposited Residue Count: 2,252
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANC27	A, B, C, D	563	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP Query on TPP Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], M [auth D]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.319 (Depositor), 0.324 (DCC)
R-Value Work: 0.246 (Depositor), 0.248 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.33	α = 90
b = 108.33	β = 90
c = 322.651	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
BALBES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-03-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-03-07
Type: Initial release
Version 1.1: 2018-04-18
Changes: Data collection, Database references
Version 1.2: 2018-11-28
Changes: Data collection, Source and taxonomy, Structure summary
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description