8YR5 | pdb_00008yr5

Crystal structure of E. coli phosphatidylserine synthase in apo state

PDB DOI: https://doi.org/10.2210/pdb8YR5/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli str. K-12 substr. MG1655
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-03-20 Released: 2024-11-20
Deposition Author(s): Kim, J., Lee, E., Cho, G.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free:
0.285 (Depositor), 0.280 (DCC)
R-Value Work:
0.242 (Depositor), 0.242 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for membrane association and catalysis by phosphatidylserine synthase in Escherichia coli.

Lee, E., Cho, G., Kim, J.

(2024) Sci Adv 10: eadq4624-eadq4624

PubMed: 39693441 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adq4624
Primary Citation Related Structures:
8YR5, 8YR6

PubMed Abstract:
Phosphatidylserine synthase (PssA) is essential in the biosynthesis of phosphatidylethanolamine, a major phospholipid of bacterial membranes. A peripheral membrane protein PssA can associate with the cellular membrane in its active state or exist in the cytosol in an inactive form. The membrane-bound enzyme acts on cytidine diphosphate diacylglycerol (CDP-DG) to form cytidine monophosphate and a covalent intermediate, which is subsequently targeted by serine to produce phosphatidylserine. Here, we present two crystal structures of Escherichia coli PssA, one complexed with CDP-DG and the other without. The lipid-bound structure mimics the Michaelis complex before the formation of a covalent intermediate, revealing key determinants for substrate recognition and catalysis. Notably, membrane-free PssA is in a monomer-dimer equilibrium, with only the monomer capable of associating with the membrane, suggesting a regulatory mechanism for phospholipid biosynthesis dependent on the oligomerization state of the enzyme.

Organizational Affiliation

Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.

Macromolecule Content

Total Structure Weight: 650.29 kDa
Atom Count: 43,895
Modeled Residue Count: 5,282
Deposited Residue Count: 5,532
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CDP-diacylglycerol--serine O-phosphatidyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	461	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0 Gene Names: pssA, pss, b2585, JW2569 EC: 2.7.8.8
UniProt
Find proteins for P23830 (Escherichia coli (strain K12)) Explore P23830 Go to UniProtKB: P23830
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23830
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain Y [auth G] SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain V [auth E] SDF format, chain U [auth E] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain JA [auth L] SDF format, chain IA [auth L] SDF format, chain HA [auth K] SDF format, chain GA [auth K] SDF format, chain FA [auth J] SDF format, chain EA [auth I] SDF format, chain DA [auth I] SDF format, chain CA [auth H] SDF format, chain BA [auth H] SDF format, chain AA [auth G] MOL2 format, chain Z [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain V [auth E] MOL2 format, chain U [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth L] MOL2 format, chain IA [auth L] MOL2 format, chain HA [auth K] MOL2 format, chain GA [auth K] MOL2 format, chain FA [auth J] MOL2 format, chain EA [auth I] MOL2 format, chain DA [auth I] MOL2 format, chain CA [auth H] MOL2 format, chain BA [auth H] MOL2 format, chain AA [auth G] mmCIF format, chain Z [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain V [auth E] mmCIF format, chain U [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth L] mmCIF format, chain IA [auth L] mmCIF format, chain HA [auth K] mmCIF format, chain GA [auth K] mmCIF format, chain FA [auth J] mmCIF format, chain EA [auth I] mmCIF format, chain DA [auth I] mmCIF format, chain CA [auth H] mmCIF format, chain BA [auth H] mmCIF format, chain AA [auth G]	AA [auth G] BA [auth H] CA [auth H] DA [auth I] EA [auth I] AA [auth G], BA [auth H], CA [auth H], DA [auth I], EA [auth I], FA [auth J], GA [auth K], HA [auth K], IA [auth L], JA [auth L], M [auth A], N [auth A], O [auth B], P [auth B], Q [auth C], R [auth C], S [auth D], T [auth D], U [auth E], V [auth E], W [auth F], X [auth F], Y [auth G], Z [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth I] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain HA [auth K] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth I] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain HA [auth K] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free: 0.285 (Depositor), 0.280 (DCC)
R-Value Work: 0.242 (Depositor), 0.242 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.04	α = 88.24
b = 94.1	β = 87.7
c = 194.75	γ = 60.07

Software Package:

Software Name	Purpose
MxDC	data collection
autoPROC	data processing
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction