4CQM

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


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 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, Oulu FI-90014, Finland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ESTRADIOL 17-BETA-DEHYDROGENASE 8
A, E, H, I, L
A, E, H, I, L, M, P
261Homo sapiensMutation(s): 0 
EC: 1.1.1.62 (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
GTEx:  ENSG00000204228 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92506
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CARBONYL REDUCTASE FAMILY MEMBER 4
B, C, F, G, J
B, C, F, G, J, K, N, O
244Homo sapiensMutation(s): 0 
EC: 1.1.1.100
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N4T8 (Homo sapiens)
Explore Q8N4T8 
Go to UniProtKB:  Q8N4T8
PHAROS:  Q8N4T8
GTEx:  ENSG00000145439 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N4T8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ESTRADIOL 17-BETA-DEHYDROGENASE 8261Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000204228 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92506
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
BA [auth G]
CA [auth H]
EA [auth I]
IA [auth J]
JA [auth K]
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
Query on GOL

Download Ideal Coordinates CCD File 
FA [auth I],
NA [auth M],
R [auth A],
X [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth F]
GA [auth I]
HA [auth I]
LA [auth L]
OA [auth M]
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
Query on ACT

Download Ideal Coordinates CCD File 
DA [auth H],
PA [auth M],
UA [auth P]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OAS
Query on OAS
D
L-PEPTIDE LINKINGC5 H9 N O4SER
Binding Affinity Annotations 
IDSourceBinding 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 = 87.501α = 90
b = 238.411β = 94.18
c = 87.688γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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