Q16836 (HCDH_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial
Short name=HCDH
EC=1.1.1.35

Alternative name(s):
Medium and short-chain L-3-hydroxyacyl-coenzyme A dehydrogenase
Short-chain 3-hydroxyacyl-CoA dehydrogenase

Gene names

Name:	HADH
Synonyms:	HAD, HADHSC, SCHAD

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	314 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Plays an essential role in the mitochondrial beta-oxidation of short chain fatty acids. Exerts it highest activity toward 3-hydroxybutyryl-CoA.
Catalytic activity	(S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH.
Pathway	Lipid metabolism; fatty acid beta-oxidation.
Subunit structure	Homodimer.
Subcellular location	Mitochondrion matrix.
Tissue specificity	Expressed in liver, kidney, pancreas, heart and skeletal muscle.
Involvement in disease	3-alpha-hydroxyacyl-CoA dehydrogenase deficiency (HADH deficiency) [MIM:231530]: A metabolic disorder with various clinical presentations including hypoglycemia, hepatoencephalopathy, myopathy or cardiomyopathy, and in some cases sudden death. Note: The disease is caused by mutations affecting the gene represented in this entry. Familial hyperinsulinemic hypoglycemia 4 (HHF4) [MIM:609975]: Most common cause of persistent hypoglycemia in infancy. Unless early and aggressive intervention is undertaken, brain damage from recurrent episodes of hypoglycemia may occur. HHF4 should be easily recognizable by analysis of acylcarnitine species and that this disorder responds well to treatment with diazoxide. It provides the first 'experiment of nature' that links impaired fatty acid oxidation to hyperinsulinism and that provides support for the concept that a lipid signaling pathway is implicated in the control of insulin secretion. Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.12
Sequence similarities	Belongs to the 3-hydroxyacyl-CoA dehydrogenase family.

Ontologies

Keywords
Biological process	Fatty acid metabolism Lipid metabolism
Cellular component	Mitochondrion
Coding sequence diversity	Alternative splicing Polymorphism
Disease	Disease mutation
Domain	Transit peptide
Ligand	NAD
Molecular function	Oxidoreductase
PTM	Acetylation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	fatty acid beta-oxidation Traceable author statement. Source: Reactome
Cellular_component	mitochondrial matrix Traceable author statement. Source: Reactome nucleus Inferred from direct assay. Source: HPA
Molecular_function	3-hydroxyacyl-CoA dehydrogenase activity Traceable author statement. Source: Reactome NAD+ binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q16836-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q16836-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MGRAGLEAPPPPCGVTGTPGARGLQGRVGPRPQSLAFRGCLPRASSLPGSPRCRRRCHTM
     236-236: R → RDFQTCGDSNSGLGFSLK

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 12

12

Mitochondrion

Chain

13 – 314

302

Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial

PRO_0000007406

Regions

Nucleotide binding

34 – 39

6

NAD

Sites

Binding site

57

1

NAD

Binding site

73

1

Coenzyme A

Binding site

80

1

Coenzyme A

Binding site

122

1

NAD

Binding site

127

1

NAD

Binding site

149

1

Coenzyme A

Binding site

149

1

NAD

Binding site

173

1

NAD

Binding site

305

1

NAD

Site

170

1

Important for catalytic activity Probable

Amino acid modifications

Modified residue

185

1

N6-acetyllysine Ref.6

Modified residue

202

1

N6-acetyllysine Ref.6

Modified residue

241

1

N6-acetyllysine Ref.6

Modified residue

312

1

N6-acetyllysine Ref.6

Natural variations

Alternative sequence

1

1

M → MGRAGLEAPPPPCGVTGTPG ARGLQGRVGPRPQSLAFRGC LPRASSLPGSPRCRRRCHTM in isoform 2.

VSP_016551

Alternative sequence

236

1

R → RDFQTCGDSNSGLGFSLK in isoform 2.

VSP_016552

Natural variant

40

1

A → T in HADH deficiency. Ref.11

VAR_024079

Natural variant

57

1

D → E in HADH deficiency. Ref.11

VAR_024080

Natural variant

86

1

L → P. Ref.1 Ref.2 Ref.3 Ref.5
Corresponds to variant rs4956145 [ dbSNP | Ensembl ].

VAR_026764

Natural variant

152

1

Q → H. Ref.1
Corresponds to variant rs1051519 [ dbSNP | Ensembl ].

VAR_055701

Natural variant

258

1

P → L in HHF4; loss of activity. Ref.12

VAR_024081

Experimental info

Isoform 2:

Sequence conflict

41

1

L → P in AAB58153. Ref.2

Sequence conflict

56

1

R → H in AAB58153. Ref.2

Secondary structure

1

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314

Helix Strand Turn

Details...

Beta strand

29 – 33

5

Helix

37 – 48

12

Beta strand

52 – 56

5

Helix

60 – 79

20

Beta strand

82 – 84

3

Helix

86 – 98

13

Beta strand

100 – 104

5

Helix

106 – 109

4

Helix

110 – 112

3

Beta strand

114 – 118

5

Helix

124 – 134

11

Turn

135 – 137

3

Beta strand

143 – 146

4

Beta strand

149 – 151

3

Helix

153 – 157

5

Helix

163 – 165

3

Beta strand

166 – 171

6

Turn

175 – 177

3

Beta strand

180 – 184

5

Helix

191 – 203

13

Beta strand

207 – 211

5

Turn

215 – 218

4

Helix

219 – 235

17

Helix

241 – 252

12

Helix

258 – 265

8

Helix

267 – 279

13

Turn

280 – 283

4

Helix

285 – 287

3

Helix

291 – 298

8

Turn

304 – 307

4

Beta strand

308 – 312

5

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified November 2, 2010. Version 3. Checksum: 0C6F7C01BBCE646A	FASTA	314	34,294
	10 20 30 40 50 60 MAFVTRQFMR SVSSSSTASA SAKKIIVKHV TVIGGGLMGA GIAQVAAATG HTVVLVDQTE 70 80 90 100 110 120 DILAKSKKGI EESLRKVAKK KFAENLKAGD EFVEKTLSTI ATSTDAASVV HSTDLVVEAI 130 140 150 160 170 180 VENLKVKNEL FKRLDKFAAE HTIFASNTSS LQITSIANAT TRQDRFAGLH FFNPVPVMKL 190 200 210 220 230 240 VEVIKTPMTS QKTFESLVDF SKALGKHPVS CKDTPGFIVN RLLVPYLMEA IRLYERGDAS 250 260 270 280 290 300 KEDIDTAMKL GAGYPMGPFE LLDYVGLDTT KFIVDGWHEM DAENPLHQPS PSLNKLVAEN 310 KFGKKTGEGF YKYK
	Isoform 2 [UniParc]. Checksum: 3C20D80AAC4EB142	FASTA	390	42,140
	10 20 30 40 50 60 MGRAGLEAPP PPCGVTGTPG ARGLQGRVGP RPQSLAFRGC LPRASSLPGS PRCRRRCHTM 70 80 90 100 110 120 AFVTRQFMRS VSSSSTASAS AKKIIVKHVT VIGGGLMGAG IAQVAAATGH TVVLVDQTED 130 140 150 160 170 180 ILAKSKKGIE ESLRKVAKKK FAENLKAGDE FVEKTLSTIA TSTDAASVVH STDLVVEAIV 190 200 210 220 230 240 ENLKVKNELF KRLDKFAAEH TIFASNTSSL QITSIANATT RQDRFAGLHF FNPVPVMKLV 250 260 270 280 290 300 EVIKTPMTSQ KTFESLVDFS KALGKHPVSC KDTPGFIVNR LLVPYLMEAI RLYERDFQTC 310 320 330 340 350 360 GDSNSGLGFS LKGDASKEDI DTAMKLGAGY PMGPFELLDY VGLDTTKFIV DGWHEMDAEN 370 380 390 PLHQPSPSLN KLVAENKFGK KTGEGFYKYK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Human short-chain L-3-hydroxyacyl-CoA dehydrogenase: cloning and characterization of the coding sequence." Vredendaal P.J.C.M., van den Berg I.E.T., Malingre H.E.M., Stroobants A.K., Oldeweghuis D.E.M., Berger R. Biochem. Biophys. Res. Commun. 223:718-723(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANTS PRO-86 AND HIS-152. Tissue: Liver.
[2]	"Cloning of a L-3-hydroxyacyl CoA dehydrogenase that binds to GLUT4 glucose transporter cytoplasmic C-terminus: possible crosstalk between glucose transport and fatty acid metabolism." Shi Y., Samuel S.J., Lee W., Yu C.H., Zhang W., Lachaal M., Jung C.Y. Submitted (NOV-1996) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 2), NUCLEOTIDE SEQUENCE [MRNA] OF 7-314 (ISOFORM 1), VARIANT PRO-86. Tissue: Skeletal muscle.
[3]	"Human short chain L-3-hydroxyacyl-CoA dehydrogenase." O'Brien L.K., Sims H.F., Strauss A.W. Submitted (SEP-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT PRO-86.
[4]	"Generation and annotation of the DNA sequences of human chromosomes 2 and 4." Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K. Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT PRO-86. Tissue: Lung.
[6]	"Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-185; LYS-202; LYS-241 AND LYS-312, MASS SPECTROMETRY.
[7]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]	"Biochemical characterization and crystal structure determination of human heart short chain L-3-hydroxyacyl-CoA dehydrogenase provide insights into catalytic mechanism." Barycki J.J., O'Brien L.K., Bratt J.M., Zhang R., Sanishvili R., Strauss A.W., Banaszak L.J. Biochemistry 38:5786-5798(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 13-314 IN COMPLEX WITH SUBSTRATE AND NAD.
[9]	"Sequestration of the active site by interdomain shifting. Crystallographic and spectroscopic evidence for distinct conformations of L-3-hydroxyacyl-CoA dehydrogenase." Barycki J.J., O'Brien L.K., Strauss A.W., Banaszak L.J. J. Biol. Chem. 275:27186-27196(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 13-314 IN COMPLEX WITH SUBSTRATE AND NAD.
[10]	"3-hydroxyacyl-CoA dehydrogenase and short chain 3-hydroxyacyl-CoA dehydrogenase in human health and disease." Yang S.-Y., He X.-Y., Schulz H. FEBS J. 272:4874-4883(2005) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.
[11]	"Fulminant hepatic failure associated with mutations in the medium and short chain L-3-hydroxyacyl-CoA dehydrogenase gene." O'Brien L.K., Rinaldo P., Sims H.F., Alonso E.M., Charrow J., Jones P.M., Bennett M.J., Barycki J.J., Banaszak L.J., Strauss A.W. J. Inherit. Metab. Dis. 23 Suppl. 1:127-127(2000) Cited for: VARIANTS HADH DEFICIENCY THR-40 AND GLU-57.
[12]	"Hyperinsulinism in short-chain L-3-hydroxyacyl-CoA dehydrogenase deficiency reveals the importance of beta-oxidation in insulin secretion." Clayton P.T., Eaton S., Aynsley-Green A., Edginton M., Hussain K., Krywawych S., Datta V., Malingre H.E.M., Berger R., van den Berg I.E.T. J. Clin. Invest. 108:457-465(2001) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT HHF4 LEU-258, CHARACTERIZATION OF VARIANT HHF4 LEU-258.
+	Additional computationally mapped references.

Web resources

GeneReviews

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X96752 mRNA. Translation: CAA65528.1.
AF001902 mRNA. Translation: AAB54008.1.
AF001903 mRNA. Translation: AAB54009.1.
AF001904 Genomic DNA. Translation: AAB58153.1.
AF095703 Genomic DNA. Translation: AAD13581.1.
AC114733 Genomic DNA. Translation: AAY41050.1.
AC118062 Genomic DNA. No translation available.
BC000306 mRNA. Translation: AAH00306.1.

IPI

IPI00294398.
IPI00298406.

PIR

JC4879.

RefSeq

NP_001171634.2. NM_001184705.2.
NP_005318.3. NM_005327.4.

UniGene

Hs.438289.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1F0Y	X-ray	1.80	A/B	13-314	[»]
1F12	X-ray	2.40	A/B	13-314	[»]
1F14	X-ray	2.30	A/B	13-314	[»]
1F17	X-ray	2.30	A/B	13-314	[»]
1IL0	X-ray	2.20	A/B	13-308	[»]
1LSJ	X-ray	2.50	A/B	13-314	[»]
1LSO	X-ray	2.60	A/B	13-314	[»]
1M75	X-ray	2.30	A/B	13-314	[»]
1M76	X-ray	2.15	A/B	13-314	[»]
2HDH	X-ray	2.20	A/B	24-314	[»]
3HAD	X-ray	2.00	A/B	13-314	[»]
3RQS	X-ray	2.00	A/B	1-314	[»]

ProteinModelPortal

Q16836.

SMR

Q16836. Positions 1-314.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q16836. 3 interactions.

MINT

MINT-5004681.

STRING

9606.ENSP00000312288.

PTM databases

PhosphoSite

Q16836.

Polymorphism databases

DMDM

311033442.

2D gel databases

REPRODUCTION-2DPAGE

IPI00298406.

UCD-2DPAGE

O00324.
Q16836.

Proteomic databases

PaxDb

Q16836.

PRIDE

Q16836.

Protocols and materials databases

DNASU

3033.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000309522; ENSP00000312288; ENSG00000138796.

GeneID

3033.

KEGG

hsa:3033.

UCSC

uc003hyq.3. human.
uc010ilx.3. human.

Organism-specific databases

CTD

3033.

GeneCards

GC04P108910.

HGNC

HGNC:4799. HADH.

HPA

HPA039588.

MIM

231530. phenotype.
601609. gene.
609975. phenotype.

neXtProt

NX_Q16836.

Orphanet

71212. Hyperinsulinism due to 3-hydroxylacyl-CoA dehydrogenase deficiency.

PharmGKB

PA29173.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG1250.

HOGENOM

HOG000141498.

HOVERGEN

HBG000832.

KO

K00022.

OrthoDB

EOG44BB2Z.

Enzyme and pathway databases

BioCyc

MetaCyc:HS06563-MONOMER.

Pathway_Interaction_DB

hnf3bpathway. FOXA2 and FOXA3 transcription factor networks.

Reactome

REACT_111217. Metabolism.

SABIO-RK

Q16836.

UniPathway

UPA00659.

Gene expression databases

ArrayExpress

Q16836.

Bgee

Q16836.

CleanEx

HS_HADH.

Genevestigator

Q16836.

GermOnline

ENSG00000138796. Homo sapiens.

Family and domain databases

Gene3D

1.10.1040.10. 1 hit.
3.40.50.720. 1 hit.

InterPro

IPR022694. 3-OHacyl-CoA_DH.
IPR006180. 3-OHacyl-CoA_DH_CS.
IPR006176. 3-OHacyl-CoA_DH_NAD-bd.
IPR006108. 3HC_DH_C.
IPR008927. 6-PGluconate_DH_C-like.
IPR013328. DH_multihelical.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

Pfam

PF00725. 3HCDH. 1 hit.
PF02737. 3HCDH_N. 1 hit.
[Graphical view]

PIRSF

PIRSF000105. HCDH. 1 hit.

SUPFAM

SSF48179. 6DGDH_C_like. 1 hit.

PROSITE

PS00067. 3HCDH. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

HADH. human.

DrugBank

DB00157. NADH.

EvolutionaryTrace

Q16836.

GenomeRNAi

3033.

NextBio

12006.

SOURCE

Search...

Entry information

Entry name

HCDH_HUMAN

Accession

Primary (citable) accession number: Q16836
Secondary accession number(s): O00324 , O00397, O00753, Q4W5B4

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 2, 2010
Last modified:	May 29, 2013
This is version 150 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.