4CQM

Crystal structure of heterotetrameric human ketoacyl reductase complexed with NAD and NADP

• PDB DOI:  https://doi.org/10.2210/pdb4CQM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-02-19 Released: 2014-09-10 
• Deposition Author(s): Venkatesan, R., SahTeli, S.K., Awoniyi, L.O., Jiang, G., Prus, P., Kastoniotis, A.J., Hiltunen, J.K., Wierenga, R.K., Chen, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.235 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 

Literature

Insights Into Mitochondrial Fatty Acid Synthesis from the Structure of Heterotetrameric 3-Ketoacyl-Acp Reductase/3R-Hydroxyacyl-Coa Dehydrogenase.

Venkatesan, R., Sah-Teli, S.K., Awoniyi, L.O., Jiang, G., Prus, P., Kastaniotis, A.J., Hiltunen, J.K., Wierenga, R.K., Chen, Z.

(2014) Nat Commun 5: 4805

• PubMed: 25203508 
• DOI: https://doi.org/10.1038/ncomms5805
• Primary Citation of Related Structures:  
  4CQL, 4CQM


• PubMed Abstract: 
  

Mitochondrial fatty acid synthesis (mtFAS) is essential for respiratory growth in yeast and mammalian embryonic survival. The human 3-ketoacyl-acyl carrier protein (ACP) reductase (KAR) of mtFAS is a heterotetrameric α2β2-assembly composed of 17β-hydroxysteroid dehydrogenase type-8 (HSD17B8, α-subunit) and carbonyl reductase type-4 (CBR4, β-subunit). Here we provide a structural explanation for the stability of the heterotetramer from the crystal structure with NAD(+) and NADP(+) bound to the HSD17B8 and CBR4 subunits, respectively, and show that the catalytic activity of the NADPH- and ACP-dependent CBR4 subunit is crucial for a functional HsKAR. Therefore, mtFAS is NADPH- and ACP dependent, employing the 3R-hydroxyacyl-ACP intermediate. HSD17B8 assists in the formation of the competent HsKAR assembly. The intrinsic NAD(+)- and CoA-dependent activity of the HSD17B8 subunit on the 3R-hydroxyacyl-CoA intermediates may indicate a role for this subunit in routing 3R-hydroxyacyl-CoA esters, potentially arising from the metabolism of unsaturated fatty acids, into the mitochondrial β-oxidation pathway.

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Organizational Affiliation: 

State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 439.36 kDa 
• Atom Count: 29,356 
• Modelled Residue Count: 3,852 
• Deposited Residue Count: 4,040 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESTRADIOL 17-BETA-DEHYDROGENASE 8	A, E, H, I, L, M, P	261	Homo sapiens	Mutation(s): 0  Gene Names: HSD17B8, FABGL, HKE6, RING2, SDR30C1 EC: 1.1.1.62 (PDB Primary Data), 1.1.1.239 (PDB Primary Data), 1.1.1.100 (PDB Primary Data), 1.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92506 (Homo sapiens) Explore Q92506  Go to UniProtKB:  Q92506
PHAROS:  Q92506

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBONYL REDUCTASE FAMILY MEMBER 4	B, C, F, G, J, K, N, O	244	Homo sapiens	Mutation(s): 0  Gene Names: CBR4, SDR45C1 EC: 1.1.1.100 (PDB Primary Data), 1.6.5.10 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N4T8 (Homo sapiens) Explore Q8N4T8  Go to UniProtKB:  Q8N4T8
PHAROS:  Q8N4T8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ESTRADIOL 17-BETA-DEHYDROGENASE 8	D	261	Homo sapiens	Mutation(s): 0  Gene Names: HSD17B8, FABGL, HKE6, RING2, SDR30C1 EC: 1.1.1.62 (PDB Primary Data), 1.1.1 (PDB Primary Data), 1.1.1.239 (PDB Primary Data), 1.1.1.100 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92506 (Homo sapiens) Explore Q92506  Go to UniProtKB:  Q92506
PHAROS:  Q92506

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	BA [auth G], CA [auth H], EA [auth I], IA [auth J], JA [auth K], KA [auth L], MA [auth M], Q [auth A], QA [auth N], RA [auth O], S [auth B], SA [auth P], T [auth C], U [auth D], W [auth E], Z [auth F]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GOL	FA [auth I], NA [auth M], R [auth A], X [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	AA [auth F], GA [auth I], HA [auth I], LA [auth L], OA [auth M], TA [auth P], V [auth D], Y [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	DA [auth H], PA [auth M], UA [auth P]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OAS	D	L-PEPTIDE LINKING	C5 H9 N O4		SER

Binding Affinity Annotations
ID	Source	Binding Affinity
NAP	Binding MOAD:  4CQM	Kd: 2.68e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.235 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.501	α = 90
b = 238.411	β = 94.18
c = 87.688	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): Venkatesan, R., SahTeli, S.K., Awoniyi, L.O., Jiang, G., Prus, P., Kastoniotis, A.J., Hiltunen, J.K., Wierenga, R.K., Chen, Z.

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2014-09-17
  Changes: Database references