3GP3 | pdb_00003gp3

Crystal structure of phosphoglyceromutase from Burkholderia pseudomallei with 2-phosphoserine

PDB DOI: https://doi.org/10.2210/pdb3GP3/pdb

Classification: ISOMERASE
Organism(s): Burkholderia pseudomallei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-20 Released: 2009-03-31
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.268 (Depositor), 0.245 (DCC)
R-Value Work:
0.237 (Depositor)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

An ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase.

Davies, D.R., Staker, B.L., Abendroth, J.A., Edwards, T.E., Hartley, R., Leonard, J., Kim, H., Rychel, A.L., Hewitt, S.N., Myler, P.J., Stewart, L.J.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1044-1050

PubMed: 21904048 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309111030405
Primary Citation Related Structures:
3EZN, 3FDZ, 3GP3, 3GP5, 3GW8, 3LNT

PubMed Abstract:
Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and Northern Australia. Burkholderia is responsible for melioidosis, a serious infection of the skin. The enzyme 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (PGAM) catalyzes the interconversion of 3-phosphoglycerate and 2-phosphoglycerate, a key step in the glycolytic pathway. As such it is an extensively studied enzyme and X-ray crystal structures of PGAM enzymes from multiple species have been elucidated. Vanadate is a phosphate mimic that is a powerful tool for studying enzymatic mechanisms in phosphoryl-transfer enzymes such as phosphoglycerate mutase. However, to date no X-ray crystal structures of phosphoglycerate mutase have been solved with vanadate acting as a substrate mimic. Here, two vanadate complexes together with an ensemble of substrate and fragment-bound structures that provide a comprehensive picture of the function of the Burkholderia enzyme are reported.

Organizational Affiliation

Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA. ddavies@embios.com

Macromolecule Content

Total Structure Weight: 118.06 kDa
Atom Count: 8,274
Modeled Residue Count: 918
Deposited Residue Count: 1,028
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase	A, B, C, D	257	Burkholderia pseudomallei	Mutation(s): 0 Gene Names: gpmA, BPSL0443 EC: 5.4.2.1 (PDB Primary Data), 5.4.2.11 (UniProt)
UniProt
Find proteins for Q3JWH7 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JWH7 Go to UniProtKB: Q3JWH7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3JWH7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A] H [auth B] K [auth C] L [auth C] O [auth D] E [auth A], H [auth B], K [auth C], L [auth C], O [auth D], P [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D]
SEP Query on SEP Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], N [auth C], R [auth D]	PHOSPHOSERINE C₃ H₈ N O₆ P BZQFBWGGLXLEPQ-REOHCLBHSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
PO3 Query on PO3 Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], M [auth C], Q [auth D]	PHOSPHITE ION O₃ P AQSJGOWTSHOLKH-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.268 (Depositor), 0.245 (DCC)
R-Value Work: 0.237 (Depositor)
R-Value Observed: 0.238 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.263	α = 107.96
b = 72.045	β = 93
c = 78.036	γ = 104.2

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-03-31

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2009-03-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-10-05
Changes: Database references
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2024-02-21
Changes: Data collection, Database references, Derived calculations