5DLV | pdb_00005dlv

Crystal structure of Autotaxin (ENPP2) with tauroursodeoxycholic acid (TUDCA)

PDB DOI: https://doi.org/10.2210/pdb5DLV/pdb

Classification: HYDROLASE
Organism(s): Rattus norvegicus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2015-09-07 Released: 2016-04-13
Deposition Author(s): Keune, W.J., Heidebrecht, T., von Castelmur, E., Joosten, R.P., Perrakis, A.
Funding Organization(s): NWO

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.227 (Depositor), 0.232 (DCC)
R-Value Work:
0.193 (Depositor), 0.200 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Steroid binding to Autotaxin links bile salts and lysophosphatidic acid signalling.

Keune, W.J., Hausmann, J., Bolier, R., Tolenaars, D., Kremer, A., Heidebrecht, T., Joosten, R.P., Sunkara, M., Morris, A.J., Matas-Rico, E., Moolenaar, W.H., Oude Elferink, R.P., Perrakis, A.

(2016) Nat Commun 7: 11248-11248

PubMed: 27075612 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/ncomms11248
Primary Citation Related Structures:
5DLT, 5DLV, 5DLW

PubMed Abstract:
Autotaxin (ATX) generates the lipid mediator lysophosphatidic acid (LPA). ATX-LPA signalling is involved in multiple biological and pathophysiological processes, including vasculogenesis, fibrosis, cholestatic pruritus and tumour progression. ATX has a tripartite active site, combining a hydrophilic groove, a hydrophobic lipid-binding pocket and a tunnel of unclear function. We present crystal structures of rat ATX bound to 7α-hydroxycholesterol and the bile salt tauroursodeoxycholate (TUDCA), showing how the tunnel selectively binds steroids. A structure of ATX simultaneously harbouring TUDCA in the tunnel and LPA in the pocket, together with kinetic analysis, reveals that bile salts act as partial non-competitive inhibitors of ATX, thereby attenuating LPA receptor activation. This unexpected interplay between ATX-LPA signalling and select steroids, notably natural bile salts, provides a molecular basis for the emerging association of ATX with disorders associated with increased circulating levels of bile salts. Furthermore, our findings suggest potential clinical implications in the use of steroid drugs.

Organizational Affiliation

Division of Biochemistry, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.

Macromolecule Content

Total Structure Weight: 199.1 kDa
Atom Count: 13,814
Modeled Residue Count: 1,562
Deposited Residue Count: 1,654
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2	A, B	827	Rattus norvegicus	Mutation(s): 2 Gene Names: c EC: 3.1.4.39 (PDB Primary Data), 3.1.4.4 (UniProt)
UniProt
Find proteins for Q64610 (Rattus norvegicus) Explore Q64610 Go to UniProtKB: Q64610
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q64610
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q64610-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	9		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G37135JQ GlyCosmos: G37135JQ GlyGen: G37135JQ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	7		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G16404YH GlyCosmos: G16404YH GlyGen: G16404YH

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5D5 Query on 5D5 Download:Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain Y [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain Y [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain Y [auth A]	AB [auth B], Y [auth A]	2-{[(3alpha,5beta,7alpha,8alpha,14beta,17alpha)-3,7-dihydroxy-24-oxocholan-24-yl]amino}ethanesulfonic acid C₂₆ H₄₅ N O₆ S BHTRKEVKTKCXOH-LBSADWJPSA-N		Interactions Focus chain AB [auth B] Focus chain Y [auth A] Interactions & Density Focus chain AB [auth B] Focus chain Y [auth A]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain TA [auth B] SDF format, chain M [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain J [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] KA [auth B] H [auth A], I [auth A], J [auth A], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], VA [auth B], WA [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain XA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain XA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain XA [auth B]	V [auth A], XA [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain V [auth A] Focus chain XA [auth B] Interactions & Density Focus chain V [auth A] Focus chain XA [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain EA [auth A] SDF format, chain EB [auth B] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain GA [auth A] SDF format, chain GB [auth B] SDF format, chain HB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain HB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain HB [auth B]	BA [auth A] CA [auth A] DA [auth A] DB [auth B] EA [auth A] BA [auth A], CA [auth A], DA [auth A], DB [auth B], EA [auth A], EB [auth B], FA [auth A], FB [auth B], GA [auth A], GB [auth B], HB [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HB [auth B] Interactions & Density Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HB [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain HA [auth B] SDF format, chain IA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B]	E [auth A], F [auth A], HA [auth B], IA [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain HA [auth B] Focus chain IA [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain HA [auth B] Focus chain IA [auth B]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain Z [auth A]	AA [auth A], BB [auth B], CB [auth B], Z [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain Z [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain JA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain JA [auth B]	G [auth A], JA [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain JA [auth B] Interactions & Density Focus chain G [auth A] Focus chain JA [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain ZA [auth B]	W [auth A], X [auth A], YA [auth B], ZA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain W [auth A] Focus chain X [auth A] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain W [auth A] Focus chain X [auth A] Focus chain YA [auth B] Focus chain ZA [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
5D5	BindingDB: 5DLV	IC50: min: 1.03e+4, max: 1.04e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.227 (Depositor), 0.232 (DCC)
R-Value Work: 0.193 (Depositor), 0.200 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.88	α = 83.84
b = 77.832	β = 79.29
c = 92.437	γ = 77.08

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Funding Organization	Location	Grant Number
NWO	Netherlands	700.10.354
NWO	Netherlands	723.013.003

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 1.1: 2016-04-27
Changes: Database references
Version 1.2: 2018-02-14
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary