4BUC | pdb_00004buc

CRYSTAL STRUCTURE OF MURD LIGASE FROM THERMOTOGA MARITIMA IN APO FORM

PDB DOI: https://doi.org/10.2210/pdb4BUC/pdb

Classification: LIGASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-06-20 Released: 2013-07-17
Deposition Author(s): Favini-Stabile, S., Contreras-Martel, C., Thielens, N., Dessen, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.197 (Depositor), 0.196 (DCC)
R-Value Work:
0.163 (Depositor)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Mreb and Murg as Scaffolds for the Cytoplasmic Steps of Peptidoglycan Biosynthesis

Favini-Stabile, S., Contreras-Martel, C., Thielens, N., Dessen, A.

(2013) Environ Microbiol 15: 3218

PubMed: 23826965 Search on PubMed
DOI: https://doi.org/10.1111/1462-2920.12171
Primary Citation Related Structures:
3ZL8, 4BUB, 4BUC

PubMed Abstract:
Peptidoglycan is a major determinant of cell shape in bacteria, and its biosynthesis involves the concerted action of cytoplasmic, membrane-associated and periplasmic enzymes. Within the cytoplasm, Mur enzymes catalyse the first steps leading to peptidoglycan precursor biosynthesis, and have been suggested as being part of a multicomponent complex that could also involve the transglycosylase MurG and the cytoskeletal protein MreB. In order to initialize the characterization of a potential Mur interaction network, we purified MurD, MurE, MurF, MurG and MreB from Thermotoga maritima and characterized their interactions using membrane blotting and surface plasmon resonance. MurD, MurE and MurF all recognize MurG and MreB, but not each other, while the two latter proteins interact. In addition, we solved the crystal structures of MurD, MurE and MurF, which indicate that their C-termini display high conformational flexibilities. The differences in Mur conformations could be important parameters for the stability of an intracytoplasmic murein biosynthesis complex.

Organizational Affiliation

Institut de Biologie Structurale (IBS), Université Grenoble I, Grenoble, France; Commissariat à l'Energie Atomique (CEA), Grenoble, France; Centre National de la Recherche Scientifique (CNRS), Grenoble, France.

Macromolecule Content

Total Structure Weight: 106.57 kDa
Atom Count: 7,253
Modeled Residue Count: 854
Deposited Residue Count: 900
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE	A, B	450	Thermotoga maritima	Mutation(s): 0 EC: 6.3.2.9
UniProt
Find proteins for Q9WY76 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WY76 Go to UniProtKB: Q9WY76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WY76
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [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] Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain C [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] Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B]	BA [auth B] CA [auth B] DA [auth B] L [auth A] M [auth A] BA [auth B], CA [auth B], DA [auth B], L [auth A], M [auth A], N [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
PO3 Query on PO3 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain AA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth B]	AA [auth B], K [auth A]	PHOSPHITE ION O₃ P AQSJGOWTSHOLKH-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain K [auth A] Interactions & Density Focus chain AA [auth B] Focus chain K [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain EA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B]	EA [auth B] FA [auth B] GA [auth B] O [auth A] P [auth A] EA [auth B], FA [auth B], GA [auth B], O [auth A], P [auth A], Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain HA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain HA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain HA [auth B]	HA [auth B], R [auth A]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain HA [auth B] Focus chain R [auth A] Interactions & Density Focus chain HA [auth B] Focus chain R [auth A]

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: 2.17 Å
R-Value Free: 0.197 (Depositor), 0.196 (DCC)
R-Value Work: 0.163 (Depositor)
R-Value Observed: 0.165 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.168	α = 90
b = 135.845	β = 98.17
c = 67.265	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
autoSHARP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-07-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-17
Type: Initial release
Version 1.1: 2013-12-18
Changes: Database references
Version 1.2: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Other, Structure summary