5KYM | pdb_00005kym

Crystal Structure of the 1-acyl-sn-glycerophosphate (LPA) acyltransferase, PlsC, from Thermotoga maritima

PDB DOI: https://doi.org/10.2210/pdb5KYM/pdb

Classification: TRANSFERASE
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2016-07-21 Released: 2017-07-26
Deposition Author(s): Robertson, R.M., Yao, J., Gajewski, S., Kumar, G., Martin, E.W., Rock, C.O., White, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.277 (Depositor), 0.250 (DCC)
R-Value Work:
0.219 (Depositor)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A two-helix motif positions the lysophosphatidic acid acyltransferase active site for catalysis within the membrane bilayer.

Robertson, R.M., Yao, J., Gajewski, S., Kumar, G., Martin, E.W., Rock, C.O., White, S.W.

(2017) Nat Struct Mol Biol 24: 666-671

PubMed: 28714993 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.3436
Primary Citation Related Structures:
5KYM

PubMed Abstract:
Phosphatidic acid (PA), the central intermediate in membrane phospholipid synthesis, is generated by two acyltransferases in a pathway conserved in all life forms. The second step in this pathway is catalyzed by 1-acyl-sn-glycerol-3-phosphate acyltransferase, called PlsC in bacteria. Here we present the crystal structure of PlsC from Thermotoga maritima, revealing an unusual hydrophobic/aromatic N-terminal two-helix motif linked to an acyltransferase αβ-domain that contains the catalytic HX ₄D motif. PlsC dictates the acyl chain composition of the 2-position of phospholipids, and the acyl chain selectivity 'ruler' is an appropriately placed and closed hydrophobic tunnel. We confirmed this by site-directed mutagenesis and membrane composition analysis of Escherichia coli cells that expressed mutant PlsC. Molecular dynamics (MD) simulations showed that the two-helix motif represents a novel substructure that firmly anchors the protein to one leaflet of the membrane. This binding mode allows the PlsC active site to acylate lysophospholipids within the membrane bilayer by using soluble acyl donors.

Organizational Affiliation

Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

Macromolecule Content

Total Structure Weight: 62.5 kDa
Atom Count: 4,138
Modeled Residue Count: 473
Deposited Residue Count: 494
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-acyl-sn-glycerol-3-phosphate acyltransferase	A, B	247	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: Tmari_1701 EC: 2.3.1.51 Membrane Entity: Yes
UniProt
Find proteins for Q9X219 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X219 Go to UniProtKB: Q9X219
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X219
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HGX Query on HGX Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A] D [auth A] E [auth A] G [auth B] H [auth B] C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	1-HEPTADECANOYL-2-TRIDECANOYL-3-GLYCEROL-PHOSPHONYL CHOLINE C₃₈ H₇₇ N O₈ P AZEAMUNCULVBPK-PSXMRANNSA-O		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
DD9 Query on DD9 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.277 (Depositor), 0.250 (DCC)
R-Value Work: 0.219 (Depositor)
R-Value Observed: 0.224 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.836	α = 90
b = 173.836	β = 90
c = 173.836	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-07-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-26
Type: Initial release
Version 1.1: 2017-08-02
Changes: Database references
Version 1.2: 2017-08-16
Changes: Database references
Version 1.3: 2024-03-06
Changes: Data collection, Database references, Refinement description