3TFL | pdb_00003tfl

LytR-Cps2a-Psr family protein with bound octaprenyl pyrophosphate lipid

PDB DOI: https://doi.org/10.2210/pdb3TFL/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-08-16 Released: 2011-10-12
Deposition Author(s): Kawai, Y., Marles-Wright, J., Cleverley, R.M., Emmins, R., Ishikawa, S., Kuwano, M., Heinz, N., Khai Bui, N., Hoyland, C.N., Ogasawara, N., Lewis, R.J., Vollmer, W., Daniel, R.A., Errington, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.242 (Depositor), 0.229 (DCC)
R-Value Work:
0.191 (Depositor)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A widespread family of bacterial cell wall assembly proteins.

Kawai, Y., Marles-Wright, J., Cleverley, R.M., Emmins, R., Ishikawa, S., Kuwano, M., Heinz, N., Bui, N.K., Hoyland, C.N., Ogasawara, N., Lewis, R.J., Vollmer, W., Daniel, R.A., Errington, J.

(2011) EMBO J 30: 4931-4941

PubMed: 21964069 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/emboj.2011.358
Primary Citation Related Structures:
2XXP, 2XXQ, 3TEL, 3TEP, 3TFL

PubMed Abstract:
Teichoic acids and acidic capsular polysaccharides are major anionic cell wall polymers (APs) in many bacteria, with various critical cell functions, including maintenance of cell shape and structural integrity, charge and cation homeostasis, and multiple aspects of pathogenesis. We have identified the widespread LytR-Cps2A-Psr (LCP) protein family, of previously unknown function, as novel enzymes required for AP synthesis. Structural and biochemical analysis of several LCP proteins suggest that they carry out the final step of transferring APs from their lipid-linked precursor to cell wall peptidoglycan (PG). In Bacillus subtilis, LCP proteins are found in association with the MreB cytoskeleton, suggesting that MreB proteins coordinate the insertion of the major polymers, PG and AP, into the cell wall.

Organizational Affiliation

Centre for Bacterial Cell Biology, Medical School, Newcastle University, Newcastle upon Tyne, UK.

Macromolecule Content

Total Structure Weight: 45.09 kDa
Atom Count: 3,107
Modeled Residue Count: 371
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
CPS2A, Integral membrane regulatory protein Wzg	A	398	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: SPC02_0004, wzg
UniProt
Find proteins for Q4K376 (Streptococcus pneumoniae) Explore Q4K376 Go to UniProtKB: Q4K376
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4K376
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZTP Query on ZTP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl trihydrogen diphosphate C₄₀ H₆₈ O₇ P₂ IKKLDISSULFFQO-DLTKSLTJSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain E [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain B [auth A]	B [auth A] D [auth A] E [auth A] F [auth A] G [auth A] B [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.242 (Depositor), 0.229 (DCC)
R-Value Work: 0.191 (Depositor)
R-Value Observed: 0.193 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.348	α = 90
b = 73.348	β = 90
c = 163.869	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-10-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-12
Type: Initial release
Version 1.1: 2013-01-09
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations