3ZLB | pdb_00003zlb

Crystal structure of phosphoglycerate kinase from Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb3ZLB/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus pneumoniae D39
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-01-30 Released: 2014-02-12
Deposition Author(s): Bernardo-Garcia, N., Hermoso, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.192 (Depositor), 0.192 (DCC)
R-Value Work:
0.145 (Depositor), 0.149 (DCC)
R-Value Observed:
0.147 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Pneumococcal phosphoglycerate kinase interacts with plasminogen and its tissue activator.

Fulde, M., Bernardo-Garcia, N., Rohde, M., Nachtigall, N., Frank, R., Preissner, K.T., Klett, J., Morreale, A., Chhatwal, G.S., Hermoso, J.A., Bergmann, S.

(2014) Thromb Haemost 111: 401-416

PubMed: 24196407 Search on PubMed
DOI: https://doi.org/10.1160/TH13-05-0421
Primary Citation Related Structures:
3ZLB

PubMed Abstract:
Streptococcus pneumoniae is not only a commensal of the nasopharyngeal epithelium, but may also cause life-threatening diseases. Immune-electron microscopy studies revealed that the bacterial glycolytic enzyme, phosphoglycerate kinase (PGK), is localised on the pneumococcal surface of both capsulated and non-capsulated strains and colocalises with plasminogen. Since pneumococci may concentrate host plasminogen (PLG) together with its activators on the bacterial cell surface to facilitate the formation of plasmin, the involvement of PGK in this process was studied. Specific binding of human or murine PLG to strain-independent PGK was documented, and surface plasmon resonance analyses indicated a high affinity interaction with the kringle domains 1-4 of PLG. Crystal structure determination of pneumococcal PGK together with peptide array analysis revealed localisation of PLG-binding site in the N-terminal region and provided structural motifs for the interaction with PLG. Based on structural analysis data, a potential interaction of PGK with tissue plasminogen activator (tPA) was proposed and experimentally confirmed by binding studies, plasmin activity assays and thrombus degradation analyses.

Organizational Affiliation

Simone Bergmann, PhD, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany, Tel.: +49 531 391 5818, Fax: +49 531 391 5854, E-mail: simone.bergmann@tu-bs.de.

Macromolecule Content

Total Structure Weight: 42.96 kDa
Atom Count: 3,418
Modeled Residue Count: 398
Deposited Residue Count: 398
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOGLYCERATE KINASE	A	398	Streptococcus pneumoniae D39	Mutation(s): 0 EC: 2.7.2.3
UniProt
Find proteins for Q04LZ5 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore Q04LZ5 Go to UniProtKB: Q04LZ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04LZ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], I [auth A], J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.192 (Depositor), 0.192 (DCC)
R-Value Work: 0.145 (Depositor), 0.149 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.347	α = 90
b = 78.227	β = 96.34
c = 59.033	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-02-12

Deposition Author(s):

Bernardo-Garcia, N.

Hermoso, J.A.

Revision History (Full details and data files)

Version 1.0: 2014-02-12
Type: Initial release
Version 1.1: 2019-02-27
Changes: Data collection, Database references, Other
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description