4KGD

High-resolution crystal structure of pyruvate oxidase from L. plantarum in complex with phosphate

PDB DOI: https://doi.org/10.2210/pdb4KGD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lactiplantibacillus plantarum JDM1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-04-29 Released: 2013-06-12
Deposition Author(s): Neumann, P., Tittmann, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.06 ?
R-Value Free: 0.150
R-Value Work: 0.127
R-Value Observed: 0.127

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Observation of a stable carbene at the active site of a thiamin enzyme.

Meyer, D., Neumann, P., Ficner, R., Tittmann, K.

(2013) Nat Chem Biol 9: 488-490

PubMed: 23748673 Search on PubMed
DOI: https://doi.org/10.1038/nchembio.1275
Primary Citation of Related Structures:
4KGD

PubMed Abstract:
Carbenes are highly reactive chemical compounds that are exploited as ligands in organometallic chemistry and are powerful organic catalysts. They were postulated to occur as transient intermediates in enzymes, yet their existence in a biological system could never be demonstrated directly. We present spectroscopic and structural data of a thiamin enzyme in a noncovalent complex with substrate, which implicate accumulation of a stable carbene as a major resonance contributor to deprotonated thiamin.

Organizational Affiliation

Albrecht-von-Haller Institute, G?ttingen Center for Molecular Biosciences, Ernst-Caspari-Haus, Georg-August University G?ttingen, G?ttingen, Germany.

Macromolecule Content

Total Structure Weight: 135.94 kDa
Atom Count: 11,890
Modelled Residue Count: 1,171
Deposited Residue Count: 1,206
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate oxidase	A, B	603	Lactiplantibacillus plantarum JDM1	Mutation(s): 0 Gene Names: JDM1_2870, pox5 EC: 1.2.3.3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain L [auth B]	C [auth A], L [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
TPP Query on TPP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B]	F [auth A], N [auth B]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain N [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain E [auth A]	E [auth A], O [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain O [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File 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 P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] 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 P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B]	G [auth A] H [auth A] I [auth A] J [auth A] P [auth B] G [auth A], H [auth A], I [auth A], J [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain M [auth B]	D [auth A], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.06 ?
R-Value Free: 0.150
R-Value Work: 0.127
R-Value Observed: 0.127
Space Group: C 2 2 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 119.28	α = 90
b = 154.16	β = 90
c = 165.47	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
SHELX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
PHENIX	phasing
SHELXL	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-06-12

Deposition Author(s):

Neumann, P.

Tittmann, K.

Revision History (Full details and data files)

Version 1.0: 2013-06-12
Type: Initial release
Version 1.1: 2013-06-26
Changes: Database references
Version 1.2: 2013-08-07
Changes: Database references
Version 1.3: 2017-11-15
Changes: Refinement description
Version 2.0: 2021-08-04
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description

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Help and Resources

4KGD

High-resolution crystal structure of pyruvate oxidase from L. plantarum in complex with phosphate

Observation of a stable carbene at the active site of a thiamin enzyme.

Entity ID: 1

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)