1GZ6 | pdb_00001gz6

(3R)-HYDROXYACYL-COA DEHYDROGENASE FRAGMENT OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE 2

PDB DOI: https://doi.org/10.2210/pdb1GZ6/pdb

Classification: DEHYDROGENASE
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2002-05-16 Released: 2003-01-24
Deposition Author(s): Haapalainen, A.M., Hiltunen, J.K., Glumoff, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.236 (Depositor), 0.230 (DCC)
R-Value Work:
0.197 (Depositor), 0.192 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Binary Structure of the Two-Domain (3R)-Hydroxyacyl-Coa Dehydrogenase from Rat Peroxisomal Multifunctional Enzyme Type 2 at 2.38 A Resolution

Haapalainen, A.M., Koski, M.K., Qin, Y.M., Hiltunen, J.K., Glumoff, T.

(2003) Structure 11: 87

PubMed: 12517343 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(02)00931-0
Primary Citation Related Structures:
1GZ6

PubMed Abstract:
The crystal structure of (3R)-hydroxyacyl-CoA dehydrogenase of rat peroxisomal multifunctional enzyme type 2 (MFE-2) was solved at 2.38 A resolution. The catalytic entity reveals an alpha/beta short chain alcohol dehydrogenase/reductase (SDR) fold and the conformation of the bound nicotinamide adenine dinucleotide (NAD(+)) found in other SDR enzymes. Of great interest is the separate COOH-terminal domain, which is not seen in other SDR structures. This domain completes the active site cavity of the neighboring monomer and extends dimeric interactions. Peroxisomal diseases that arise because of point mutations in the dehydrogenase-coding region of the MFE-2 gene can be mapped to changes in amino acids involved in NAD(+) binding and protein dimerization.

Organizational Affiliation

Biocenter Oulu and Department of Biochemistry, University of Oulu, P.O. Box 3000, FIN-90014 University of Oulu, Oulu, Finland.

Macromolecule Content

Total Structure Weight: 142.43 kDa
Atom Count: 9,961
Modeled Residue Count: 1,171
Deposited Residue Count: 1,276
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESTRADIOL 17 BETA-DEHYDROGENASE 4	A, B, C, D	319	Rattus norvegicus	Mutation(s): 0 EC: 1.1.1.62
UniProt
Find proteins for P97852 (Rattus norvegicus) Explore P97852 Go to UniProtKB: P97852
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P97852
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain M [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	H [auth A], I [auth B], J [auth C], M [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain M [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain K [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], K [auth D], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth D] Focus chain L [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.236 (Depositor), 0.230 (DCC)
R-Value Work: 0.197 (Depositor), 0.192 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.466	α = 90
b = 82.748	β = 94.2
c = 95.745	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-01-24

Deposition Author(s):

Haapalainen, A.M.

Hiltunen, J.K.

Glumoff, T.

Revision History (Full details and data files)

Version 1.0: 2003-01-24
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Other, Structure summary