3Q3V

Crystal structure of Phosphoglycerate Kinase from Campylobacter jejuni.

PDB DOI: https://doi.org/10.2210/pdb3Q3V/pdb

Classification: TRANSFERASE
Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-12-22 Released: 2011-01-12
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.237
R-Value Work: 0.187
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structures of putative phosphoglycerate kinases from B. anthracis and C. jejuni.

Zheng, H., Filippova, E.V., Tkaczuk, K.L., Dworzynski, P., Chruszcz, M., Porebski, P.J., Wawrzak, Z., Onopriyenko, O., Kudritska, M., Grimshaw, S., Savchenko, A., Anderson, W.F., Minor, W.

(2012) J Struct Funct Genomics 13: 15-26

PubMed: 22403005 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1007/s10969-012-9131-9
Primary Citation of Related Structures:
3Q3V, 3UWD

PubMed Abstract:
Phosphoglycerate kinase (PGK) is indispensable during glycolysis for anaerobic glucose degradation and energy generation. Here we present comprehensive structure analysis of two putative PGKs from Bacillus anthracis str. Sterne and Campylobacter jejuni in the context of their structural homologs. They are the first PGKs from pathogenic bacteria reported in the Protein Data Bank. The crystal structure of PGK from Bacillus anthracis str. Sterne (BaPGK) has been determined at 1.68 Å while the structure of PGK from Campylobacter jejuni (CjPGK) has been determined at 2.14 Å resolution. The proteins' monomers are composed of two domains, each containing a Rossmann fold, hinged together by a helix which can be used to adjust the relative position between two domains. It is also shown that apo-forms of both BaPGK and CjPGK adopt open conformations as compared to the substrate and ATP bound forms of PGK from other species.

Organizational Affiliation

Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA.

Macromolecule Content

Total Structure Weight: 89.61 kDa
Atom Count: 6,417
Modelled Residue Count: 786
Deposited Residue Count: 806
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate kinase	A, B	403	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0 Gene Names: Cj1402c, pgk EC: 2.7.2.3
UniProt
Find proteins for Q9PMQ5 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PMQ5 Go to UniProtKB: Q9PMQ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9PMQ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B]	G [auth A], N [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B]	F [auth A], M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B]	E [auth A], J [auth B], K [auth B], L [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B]	C [auth A], D [auth A], H [auth B], I [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.237
R-Value Work: 0.187
R-Value Observed: 0.190
Space Group: P 2₁ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M3ZP41

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.28	α = 90
b = 165.22	β = 90
c = 54.596	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
CCP4	model building
MrBUMP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
CCP4	phasing