1IUQ | pdb_00001iuq

The 1.55 A Crystal Structure of Glycerol-3-Phosphate Acyltransferase

PDB DOI: https://doi.org/10.2210/pdb1IUQ/pdb

Classification: TRANSFERASE
Organism(s): Cucurbita moschata
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2002-03-06 Released: 2003-10-07
Deposition Author(s): Tamada, T., Feese, M.D., Kato, Y., Kuroki, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.219 (Depositor)
R-Value Work:
0.201 (Depositor), 0.204 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Substrate recognition and selectivity of plant glycerol-3-phosphate acyltransferases (GPATs) from Cucurbita moscata and Spinacea oleracea.

Tamada, T., Feese, M.D., Ferri, S.R., Kato, Y., Yajima, R., Toguri, T., Kuroki, R.

(2004) Acta Crystallogr D Biol Crystallogr 60: 13-21

PubMed: 14684887 Search on PubMed
DOI: https://doi.org/10.1107/s0907444903020778
Primary Citation Related Structures:
1IUQ

PubMed Abstract:
Stromal glycerol-3-phosphate acyltransferases (GPAT) are responsible for the selective incorporation of saturated and unsaturated fatty-acyl chains into chloroplast membranes, which is an important determinant of a plant's ability to tolerate chilling temperatures. The molecular mechanisms of plant chilling tolerance were elucidated by creating chimeric GPATs between squash (Cucurbita moscata, chilling-sensitive) and spinach (Spinacea oleracea, chilling-tolerant) and the results were interpreted using structural information on squash GPAT determined by X-ray crystallography at 1.55 A resolution. Enzymatic analysis of the chimeric GPATs showed that the chimeric GPATs containing the spinach region from residues 128 to 187 prefer the 18:1 unsaturated fatty acid rather than 16:0 saturated fatty acid. Structure analysis suggests that the size and character of the cavity that is formed from this region determines the specific recognition of acyl chains.

Organizational Affiliation

Central Laboratories for Key Technology, Kirin Brewery Co. Ltd, Fukuura 1-13-5, Kanazawa-ku, Yokohama 236-0004, Japan.

Macromolecule Content

Total Structure Weight: 42.2 kDa
Atom Count: 3,247
Modeled Residue Count: 357
Deposited Residue Count: 367
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol-3-Phosphate Acyltransferase	A	367	Cucurbita moschata	Mutation(s): 7 EC: 2.3.1.15
UniProt
Find proteins for P10349 (Cucurbita moschata) Explore P10349 Go to UniProtKB: P10349
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10349
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.219 (Depositor)
R-Value Work: 0.201 (Depositor), 0.204 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.138	α = 90
b = 63.604	β = 90
c = 115.862	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
REFMAC	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-10-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-10-07
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-10-09
Changes: Structure summary