6SBJ

X-ray structure of mus musculus Fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) apo-form uuncomplexed

PDB DOI: https://doi.org/10.2210/pdb6SBJ/pdb

Classification: HYDROLASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-21 Released: 2020-02-26
Deposition Author(s): Rupp, B., Naschberger, A., Weiss, A.K.H.
Funding Organization(s): European Commission, Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.257
R-Value Work: 0.193
R-Value Observed: 0.196

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural and functional comparison of fumarylacetoacetate domain containing protein 1 in human and mouse.

Weiss, A.K.H., Naschberger, A., Cappuccio, E., Metzger, C., Mottes, L., Holzknecht, M., von Velsen, J., Bowler, M.W., Rupp, B., Jansen-Durr, P.

(2020) Biosci Rep 40

PubMed: 32068790 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1042/BSR20194431
Primary Citation of Related Structures:
6SBI, 6SBJ

PubMed Abstract:
FAH domain containing protein 1 (FAHD1) is a mammalian mitochondrial protein, displaying bifunctionality as acylpyruvate hydrolase (ApH) and oxaloacetate decarboxylase (ODx) activity. We report the crystal structure of mouse FAHD1 and structural mapping of the active site of mouse FAHD1. Despite high structural similarity with human FAHD1, a rabbit monoclonal antibody (RabMab) could be produced that is able to recognize mouse FAHD1, but not the human form, whereas a polyclonal antibody recognized both proteins. Epitope mapping in combination with our deposited crystal structures revealed that the epitope overlaps with a reported SIRT3 deacetylation site in mouse FAHD1.

Organizational Affiliation

University of Innsbruck, Research Institute for Biomedical Aging Research, Rennweg 10, Innsbruck A-6020, Austria.

Macromolecule Content

Total Structure Weight: 118.01 kDa
Atom Count: 6,625
Modelled Residue Count: 832
Deposited Residue Count: 1,060
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acylpyruvase FAHD1, mitochondrial	A, B, C, D	265	Mus musculus	Mutation(s): 0 Gene Names: Fahd1, MNCb-4134 EC: 3.7.1.5 (PDB Primary Data), 4.1.1.112 (PDB Primary Data), 5.3.2.2 (UniProt)
UniProt
Find proteins for Q8R0F8 (Mus musculus) Explore Q8R0F8 Go to UniProtKB: Q8R0F8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8R0F8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A] H [auth A] J [auth B] L [auth C] M [auth C] G [auth A], H [auth A], J [auth B], L [auth C], M [auth C], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain I [auth B]	E [auth A] F [auth A] I [auth B] K [auth C] N [auth D] E [auth A], F [auth A], I [auth B], K [auth C], N [auth D], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.257
R-Value Work: 0.193
R-Value Observed: 0.196
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.15151/ESRF-DC-186917546

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.401	α = 90
b = 69.959	β = 92.25
c = 107.557	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-02-26

Deposition Author(s):

Rupp, B.

Naschberger, A.

Weiss, A.K.H.

Funding Organization	Location	Grant Number
European Commission	Austria	512020
Austrian Science Fund	Austria	P28395-B26

Revision History (Full details and data files)

Version 1.0: 2020-02-26
Type: Initial release
Version 1.1: 2020-03-11
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description