5PGM | pdb_00005pgm

SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE

PDB DOI: https://doi.org/10.2210/pdb5PGM/pdb

Classification: ISOMERASE
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 1998-08-19 Released: 1999-02-16
Deposition Author(s): Rigden, D.J., Phillips, S.E.V., Fothergill-Gilmore, L.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.228 (Depositor)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Sulphate ions observed in the 2.12 A structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism.

Rigden, D.J., Walter, R.A., Phillips, S.E., Fothergill-Gilmore, L.A.

(1999) J Mol Biology 286: 1507-1517

PubMed: 10064712 Search on PubMed
DOI: https://doi.org/10.1006/jmbi.1999.2566
Primary Citation Related Structures:
5PGM

PubMed Abstract:
The structure of a new crystal form of Saccharomyces cerevisiae phosphoglycerate mutase has been solved and refined to 2.12 A with working and free R-factors of 19.7 and 22.9 %, respectively. Higher-resolution data and greater non-crystallographic symmetry have produced a more accurate protein structure than previously. Prominent among the differences from the previous structure is the presence of two sulphate ions within each active site cleft. The separation of the sulphates suggests that they may occupy the same sites as phospho groups of the bisphosphate ligands of the enzyme. Plausible binding modes for 2,3-bisphosphoglycerate and 1, 3-bisphosphoglycerate are thereby suggested. These results support previous conclusions from mutant studies, highlight interesting new targets for mutagenesis and suggest a possible mechanism of enzyme phosphorylation.

Organizational Affiliation

School of Biochemistry and Molecular Biology, Astbury Building, University of Leeds, Leeds, LS2 9JT, UK.

Macromolecule Content

Total Structure Weight: 221.77 kDa
Atom Count: 16,692
Modeled Residue Count: 1,877
Deposited Residue Count: 1,968
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOGLYCERATE MUTASE 1	A [auth D] B [auth C] C [auth A] D [auth B] E A [auth D], B [auth C], C [auth A], D [auth B], E, F, G, H	246	Saccharomyces cerevisiae	Mutation(s): 0 EC: 5.4.2.1 (PDB Primary Data), 5.4.2.11 (UniProt)
UniProt
Find proteins for P00950 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00950 Go to UniProtKB: P00950
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00950
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth E] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain U [auth F] SDF format, chain V [auth G] SDF format, chain W [auth G] SDF format, chain X [auth H] SDF format, chain Y [auth H] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth H] mmCIF format, chain I [auth D] mmCIF format, chain J [auth D] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain U [auth F] mmCIF format, chain V [auth G] mmCIF format, chain W [auth G] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth H]	I [auth D] J [auth D] K [auth C] L [auth C] M [auth A] I [auth D], J [auth D], K [auth C], L [auth C], M [auth A], N [auth A], O [auth B], P [auth B], Q [auth E], R [auth E], T [auth F], U [auth F], V [auth G], W [auth G], X [auth H], Y [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth E] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H] Interactions & Density Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth E] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H]
ALA Query on ALA Download:Ideal Coordinates CCD File SDF format, chain S [auth E] MOL2 format, chain S [auth E] mmCIF format, chain S [auth E]	S [auth E]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain S [auth E] Interactions & Density Focus chain S [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.228 (Depositor)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.497	α = 90
b = 93.262	β = 90.15
c = 147.329	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1999-02-16

Deposition Author(s):

Rigden, D.J.

Phillips, S.E.V.

Fothergill-Gilmore, L.A.

Revision History (Full details and data files)

Version 1.0: 1999-02-16
Type: Initial release
Version 1.1: 2008-03-25
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-09
Changes: Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-12-25
Changes: Advisory, Data collection, Derived calculations, Structure summary

5PGM | pdb_00005pgm

SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE

Literature

Sulphate ions observed in the 2.12 A structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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