6BMS | pdb_00006bms

Palmitoyltransferase structure

PDB DOI: https://doi.org/10.2210/pdb6BMS/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Danio rerio
Expression System: Komagataella phaffii GS115
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2017-11-15 Released: 2018-01-10
Deposition Author(s): Kumar, P., Rajashankar, K.
Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free:
0.261 (Depositor), 0.262 (DCC)
R-Value Work:
0.233 (Depositor), 0.234 (DCC)
R-Value Observed:
0.234 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Fatty acyl recognition and transfer by an integral membraneS-acyltransferase.

Rana, M.S., Kumar, P., Lee, C.J., Verardi, R., Rajashankar, K.R., Banerjee, A.

(2018) Science 359

PubMed: 29326245 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.aao6326
Primary Citation Related Structures:
6BML, 6BMM, 6BMN, 6BMS

PubMed Abstract:
DHHC (Asp-His-His-Cys) palmitoyltransferases are eukaryotic integral membrane enzymes that catalyze protein palmitoylation, which is important in a range of physiological processes, including small guanosine triphosphatase (GTPase) signaling, cell adhesion, and neuronal receptor scaffolding. We present crystal structures of two DHHC palmitoyltransferases and a covalent intermediate mimic. The active site resides at the membrane-cytosol interface, which allows the enzyme to catalyze thioester-exchange chemistry by using fatty acyl-coenzyme A and explains why membrane-proximal cysteines are candidates for palmitoylation. The acyl chain binds in a cavity formed by the transmembrane domain. We propose a mechanism for acyl chain-length selectivity in DHHC enzymes on the basis of cavity mutants with preferences for shorter and longer acyl chains.

Organizational Affiliation

Cell Biology and Neurobiology Branch, National Institutes of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content

Total Structure Weight: 83.74 kDa
Atom Count: 4,863
Modeled Residue Count: 563
Deposited Residue Count: 682
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Palmitoyltransferase	A, B [auth D]	341	Danio rerio	Mutation(s): 1 Gene Names: zdhhc15b EC: 2.3.1.225 (PDB Primary Data), 2.3.1 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for F1QXD3 (Danio rerio) Explore F1QXD3 Go to UniProtKB: F1QXD3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F1QXD3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain M [auth D] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth D] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth D] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], M [auth D], Q [auth D]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth D] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth D] Focus chain Q [auth D]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain H [auth A] MOL2 format, chain N [auth D] MOL2 format, chain H [auth A] mmCIF format, chain N [auth D] mmCIF format, chain H [auth A]	H [auth A], N [auth D]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth D] Interactions & Density Focus chain H [auth A] Focus chain N [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth D] SDF format, chain O [auth D] MOL2 format, chain J [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] mmCIF format, chain J [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D]	J [auth A], O [auth D], P [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain J [auth A] Focus chain O [auth D] Focus chain P [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], K [auth D], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth D] Focus chain L [auth D]