4O6N

Structure of AF2299, a CDP-alcohol phosphotransferase (CDP-bound)

PDB DOI: https://doi.org/10.2210/pdb4O6N/pdb

Classification: TRANSFERASE
Organism(s): Archaeoglobus fulgidus DSM 4304
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2013-12-22 Released: 2014-05-14
Deposition Author(s): Clarke, O.B., Sciara, G., Tomasek, D., Banerjee, S., Rajashankar, K.R., Shapiro, L., Mancia, F., New York Consortium on Membrane Protein Structure (NYCOMPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.262
R-Value Work: 0.226
R-Value Observed: 0.228

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis for catalysis in a CDP-alcohol phosphotransferase.

Sciara, G., Clarke, O.B., Tomasek, D., Kloss, B., Tabuso, S., Byfield, R., Cohn, R., Banerjee, S., Rajashankar, K.R., Slavkovic, V., Graziano, J.H., Shapiro, L., Mancia, F.

(2014) Nat Commun 5: 4068-4068

PubMed: 24923293 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/ncomms5068
Primary Citation of Related Structures:
4O6M, 4O6N, 4Q7C

PubMed Abstract:
The CDP-alcohol phosphotransferase (CDP-AP) family of integral membrane enzymes catalyses the transfer of a substituted phosphate group from a CDP-linked donor to an alcohol acceptor. This is an essential reaction for phospholipid biosynthesis across all kingdoms of life, and it is catalysed solely by CDP-APs. Here we report the 2.0 Å resolution crystal structure of a representative CDP-AP from Archaeoglobus fulgidus. The enzyme (AF2299) is a homodimer, with each protomer consisting of six transmembrane helices and an N-terminal cytosolic domain. A polar cavity within the membrane accommodates the active site, lined with the residues from an absolutely conserved CDP-AP signature motif (D(1)xxD(2)G(1)xxAR...G(2)xxxD(3)xxxD(4)). Structures in the apo, CMP-bound, CDP-bound and CDP-glycerol-bound states define functional roles for each of these eight conserved residues and allow us to propose a sequential, base-catalysed mechanism universal for CDP-APs, in which the fourth aspartate (D4) acts as the catalytic base.

Organizational Affiliation

1] Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA [2].

Macromolecule Content

Total Structure Weight: 89 kDa
Atom Count: 5,584
Modelled Residue Count: 674
Deposited Residue Count: 744
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AF2299, a CDP-alcohol phosphotransferase	A, B	372	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0 Gene Names: AF2299, AF_2299 Membrane Entity: Yes
UniProt
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 Group	O27985
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDP Query on CDP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B]	E [auth A], N [auth B]	CYTIDINE-5'-DIPHOSPHATE C₉ H₁₅ N₃ O₁₁ P₂ ZWIADYZPOWUWEW-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B]
MPG Query on MPG Download Ideal Coordinates CCD File SDF format, chain F [auth A] 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 O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain F [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 O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain F [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 O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], O [auth B], P [auth B], Q [auth B], R [auth B]	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate C₂₁ H₄₀ O₄ JPJYKWFFJCWMPK-GDCKJWNLSA-N		Interactions 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 O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density 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 O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B] mmCIF format, chain K [auth A] mmCIF format, chain S [auth B]	K [auth A], S [auth B]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain K [auth A] Focus chain S [auth B] Interactions & Density Focus chain K [auth A] Focus chain S [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	C [auth A], D [auth A], L [auth B], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.262
R-Value Work: 0.226
R-Value Observed: 0.228
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.329	α = 90
b = 90.67	β = 92.07
c = 106.444	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
SHELXD	phasing
SHARP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-05-14

Deposition Author(s):

New York Consortium on Membrane Protein Structure (NYCOMPS)

Revision History (Full details and data files)

Version 1.0: 2014-05-14
Type: Initial release
Version 1.1: 2014-05-21
Changes: Database references, Structure summary
Version 1.2: 2014-08-13
Changes: Database references
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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4O6N

Structure of AF2299, a CDP-alcohol phosphotransferase (CDP-bound)

Structural basis for catalysis in a CDP-alcohol phosphotransferase.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)