5D92

Structure of a phosphatidylinositolphosphate (PIP) synthase from Renibacterium Salmoninarum

PDB DOI: https://doi.org/10.2210/pdb5D92/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Archaeoglobus fulgidus DSM 4304, Renibacterium salmoninarum ATCC 33209
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2015-08-18 Released: 2015-11-04
Deposition Author(s): Clarke, O.B., Tomasek, D.T., Jorge, C.D., Belcher Dufrisne, M., Kim, M., Banerjee, S., Rajashankar, K.R., Hendrickson, W.A., Santos, H., Mancia, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.62 Å
R-Value Free: 0.300
R-Value Work: 0.280
R-Value Observed: 0.281

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis for phosphatidylinositol-phosphate biosynthesis.

Clarke, O.B., Tomasek, D., Jorge, C.D., Dufrisne, M.B., Kim, M., Banerjee, S., Rajashankar, K.R., Shapiro, L., Hendrickson, W.A., Santos, H., Mancia, F.

(2015) Nat Commun 6: 8505-8505

PubMed: 26510127 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/ncomms9505
Primary Citation of Related Structures:
5D91, 5D92

PubMed Abstract:
Phosphatidylinositol is critical for intracellular signalling and anchoring of carbohydrates and proteins to outer cellular membranes. The defining step in phosphatidylinositol biosynthesis is catalysed by CDP-alcohol phosphotransferases, transmembrane enzymes that use CDP-diacylglycerol as donor substrate for this reaction, and either inositol in eukaryotes or inositol phosphate in prokaryotes as the acceptor alcohol. Here we report the structures of a related enzyme, the phosphatidylinositol-phosphate synthase from Renibacterium salmoninarum, with and without bound CDP-diacylglycerol to 3.6 and 2.5 Å resolution, respectively. These structures reveal the location of the acceptor site, and the molecular determinants of substrate specificity and catalysis. Functional characterization of the 40%-identical ortholog from Mycobacterium tuberculosis, a potential target for the development of novel anti-tuberculosis drugs, supports the proposed mechanism of substrate binding and catalysis. This work therefore provides a structural and functional framework to understand the mechanism of phosphatidylinositol-phosphate biosynthesis.

Organizational Affiliation

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.

Macromolecule Content

Total Structure Weight: 163.01 kDa
Atom Count: 10,844
Modelled Residue Count: 1,358
Deposited Residue Count: 1,368
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AF2299 protein,Phosphatidylinositol synthase	A [auth D], B [auth A], C [auth B], D [auth C]	342	Archaeoglobus fulgidus DSM 4304, Renibacterium salmoninarum ATCC 33209 This entity is chimeric	Mutation(s): 0 Gene Names: AF_2299, RSal33209_2010 EC: 2.7.8 Membrane Entity: Yes
UniProt
Find proteins for A9WSF5 (Renibacterium salmoninarum (strain ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235)) Explore A9WSF5 Go to UniProtKB: A9WSF5
Find proteins for O27985 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O27985 Go to UniProtKB: O27985
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	A9WSF5O27985
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
58A Query on 58A Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain MA [auth B] SDF format, chain S [auth D] SDF format, chain WA [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain S [auth D] MOL2 format, chain WA [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain S [auth D] mmCIF format, chain WA [auth C]	DA [auth A], MA [auth B], S [auth D], WA [auth C]	5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9E)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine C₄₈ H₈₅ N₃ O₁₅ P₂ WVVFFOKRFKIBHD-ZIPNUMAKSA-N		Interactions Focus chain DA [auth A] Focus chain MA [auth B] Focus chain S [auth D] Focus chain WA [auth C] Interactions & Density Focus chain DA [auth A] Focus chain MA [auth B] Focus chain S [auth D] Focus chain WA [auth C]
8K6 Query on 8K6 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain E [auth D] SDF format, chain EA [auth B] SDF format, chain F [auth D] SDF format, chain FA [auth B] SDF format, chain G [auth D] SDF format, chain GA [auth B] SDF format, chain H [auth D] SDF format, chain HA [auth B] SDF format, chain I [auth D] SDF format, chain IA [auth B] SDF format, chain J [auth D] SDF format, chain JA [auth B] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain NA [auth C] SDF format, chain O [auth D] SDF format, chain OA [auth C] SDF format, chain P [auth D] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain E [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth D] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth D] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth D] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain E [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth D] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth D] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth D] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] E [auth D] EA [auth B] F [auth D] FA [auth B] AA [auth A], E [auth D], EA [auth B], F [auth D], FA [auth B], G [auth D], GA [auth B], H [auth D], HA [auth B], I [auth D], IA [auth B], J [auth D], JA [auth B], K [auth D], L [auth D], M [auth D], N [auth D], NA [auth C], O [auth D], OA [auth C], P [auth D], PA [auth C], QA [auth C], RA [auth C], SA [auth C], T [auth A], TA [auth C], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	Octadecane C₁₈ H₃₈ RZJRJXONCZWCBN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain E [auth D] Focus chain EA [auth B] Focus chain F [auth D] Focus chain FA [auth B] Focus chain G [auth D] Focus chain GA [auth B] Focus chain H [auth D] Focus chain HA [auth B] Focus chain I [auth D] Focus chain IA [auth B] Focus chain J [auth D] Focus chain JA [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain NA [auth C] Focus chain O [auth D] Focus chain OA [auth C] Focus chain P [auth D] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain E [auth D] Focus chain EA [auth B] Focus chain F [auth D] Focus chain FA [auth B] Focus chain G [auth D] Focus chain GA [auth B] Focus chain H [auth D] Focus chain HA [auth B] Focus chain I [auth D] Focus chain IA [auth B] Focus chain J [auth D] Focus chain JA [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain NA [auth C] Focus chain O [auth D] Focus chain OA [auth C] Focus chain P [auth D] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain UA [auth C] SDF format, chain VA [auth C] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C]	BA [auth A] CA [auth A] KA [auth B] LA [auth B] Q [auth D] BA [auth A], CA [auth A], KA [auth B], LA [auth B], Q [auth D], R [auth D], UA [auth C], VA [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain CA [auth A] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain UA [auth C] Focus chain VA [auth C] Interactions & Density Focus chain BA [auth A] Focus chain CA [auth A] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain UA [auth C] Focus chain VA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.62 Å
R-Value Free: 0.300
R-Value Work: 0.280
R-Value Observed: 0.281
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.002	α = 90
b = 62.489	β = 99.77
c = 169.759	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-11-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-11-04
Type: Initial release
Version 1.1: 2015-11-11
Changes: Database references
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary