1B93

METHYLGLYOXAL SYNTHASE FROM ESCHERICHIA COLI

PDB DOI: https://doi.org/10.2210/pdb1B93/pdb

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

Deposited: 1999-02-23 Released: 1999-03-16
Deposition Author(s): Saadat, D., Harrison, D.H.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.202
R-Value Work: 0.181
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of methylglyoxal synthase from Escherichia coli.

Saadat, D., Harrison, D.H.

(1999) Structure 7: 309-317

PubMed: 10368300 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(99)80041-0
Primary Citation of Related Structures:
1B93

PubMed Abstract:
The reaction mechanism of methylglyoxal synthase (MGS) is believed to be similar to that of triosephosphate isomerase (TIM). Both enzymes utilise dihydroxyacetone phosphate (DHAP) to form an enediol(ate) phosphate intermediate as the first step of their reaction pathways. However, the second catalytic step in the MGS reaction pathway is characterized by the elimination of phosphate and collapse of the enediol(ate) to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate.

Organizational Affiliation

Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.

Macromolecule Content

Total Structure Weight: 51.23 kDa
Atom Count: 3,639
Modelled Residue Count: 443
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (METHYLGLYOXAL SYNTHASE)	A, B, C	152	Escherichia coli	Mutation(s): 0 Gene Names: MGSA EC: 4.2.3.3
UniProt
Find proteins for P0A731 (Escherichia coli (strain K12)) Explore P0A731 Go to UniProtKB: P0A731
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A731
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth C] D [auth A], E [auth A], F [auth A], H [auth B], I [auth C], J [auth C], K [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.202
R-Value Work: 0.181
R-Value Observed: 0.181
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.34	α = 90
b = 123.34	β = 90
c = 155.98	γ = 120

Software Package:

Software Name	Purpose
XTALVIEW	refinement
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 1999-03-16

Deposition Author(s):

Saadat, D.

Harrison, D.H.T.

Revision History (Full details and data files)

Version 1.0: 1999-03-16
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations

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Help and Resources

1B93

METHYLGLYOXAL SYNTHASE FROM ESCHERICHIA COLI

The crystal structure of methylglyoxal synthase from Escherichia coli.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)