Reviewed, UniProtKB/Swiss-Prot Q92947 (GCDH_HUMAN)

Names and origin

Protein names

Recommended name:
    Glutaryl-CoA dehydrogenase, mitochondrial
      Short name=GCD
    EC=1.3.99.7

Gene names

Name:

GCDH

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	438 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	Catalyzes the oxidative decarboxylation of glutaryl-CoA to crotonyl-CoA and CO2 in the degradative pathway of L-lysine, L-hydroxylysine, and L-tryptophan metabolism. It uses electron transfer flavoprotein as its electron acceptor. The short isoform is inactive.
Catalytic activity	Glutaryl-CoA + acceptor = crotonoyl-CoA + CO2 + reduced acceptor.
Cofactor	FAD.
Pathway	Amino-acid metabolism; lysine degradation. Amino-acid metabolism; tryptophan metabolism.
Subunit structure	Homotetramer. Ref.9 Ref.13
Subcellular location	Mitochondrion matrix.
Tissue specificity	The 2 isoforms have been found in fibroblasts and liver.
Involvement in disease	Defects in GCDH are the cause of glutaric aciduria type 1 (GA1) [MIM:231670]. GA1 is an autosomal recessive metabolic disorder characterized by progressive dystonia and athetosis due to gliosis and neuronal loss in the basal ganglia. Ref.13 Ref.2 Ref.3 Ref.11 Ref.12
Sequence similarities	Belongs to the acyl-CoA dehydrogenase family.

Ontologies

Keywords
Cellular component	Mitochondrion
Coding sequence diversity	Alternative splicing Polymorphism
Disease	Disease mutation Glutaricaciduria
Domain	Transit peptide
Ligand	FAD Flavoprotein
Molecular function	Oxidoreductase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	mitochondrial matrix Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	FAD binding Inferred from electronic annotation. Source: InterPro electron carrier activity Inferred from electronic annotation. Source: InterPro glutaryl-CoA dehydrogenase activity Ref.2 Traceable author statement. Source: ProtInc protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
GRB2	P62993	1	EBI-1236978,EBI-401755

Alternative products

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

Isoform Long (identifier: Q92947-1)

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 Short (identifier: Q92947-2)

The sequence of this isoform differs from the canonical sequence as follows:
     415-438: GTHDIHALILGRAITGIQAFTASK → VVQMCSLKRRWNSL

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 44

44

Mitochondrion Potential

Chain

45 – 438

394

Glutaryl-CoA dehydrogenase, mitochondrial

PRO_0000000526

Regions

Nucleotide binding

177 – 180

4

FAD

Nucleotide binding

212 – 214

3

FAD

Region

138 – 139

2

Substrate binding

Region

287 – 291

5

Substrate binding

Sites

Active site

414

1

Proton acceptor Probable

Binding site

186

1

FAD

Binding site

186

1

Substrate; via carbonyl oxygen

Binding site

294

1

Substrate

Binding site

416

1

FAD

Binding site

434

1

FAD; via carbonyl oxygen

Natural variations

Alternative sequence

415 – 438

24

GTHDI…FTASK → VVQMCSLKRRWNSL in isoform Short.

VSP_000145

Natural variant

88

1

R → C in GA1.

VAR_000366

Natural variant

94

1

R → L in GA1.

VAR_000367

Natural variant

101

1

G → R in GA1. Ref.12

VAR_000368

Natural variant

115

1

C → Y in GA1.

VAR_000369

Natural variant

122

1

A → V in GA1.

VAR_000370

Natural variant

128

1

R → G in GA1.

VAR_000371

Natural variant

138

1

R → G in GA1; impaired protein stability and loss of activity. Ref.13

VAR_000372

Natural variant

139

1

S → L in GA1.

VAR_000373

Natural variant

148

1

V → I in GA1.

VAR_000374

Natural variant

161

1

R → Q in GA1.

VAR_000375

Natural variant

178

1

G → R in GA1.

VAR_000376

Natural variant

179

1

L → R in GA1.

VAR_000377

Natural variant

191

1

M → T in GA1.

VAR_000378

Natural variant

195

1

A → T in GA1.

VAR_000379

Natural variant

227

1

R → P in GA1.

VAR_000380

Natural variant

236

1

F → L in GA1.

VAR_000381

Natural variant

257

1

R → Q in GA1.

VAR_000382

Natural variant

257

1

R → W in GA1.

VAR_000383

Natural variant

266

1

M → V in GA1.

VAR_000384

Natural variant

278

1

P → S in GA1.

VAR_000385

Natural variant

283

1

L → P in GA1. Ref.12

VAR_000386

Natural variant

293

1

A → T in GA1. Ref.12

VAR_000387

Natural variant

294

1

R → W in GA1.

VAR_000388

Natural variant

295

1

Y → H in GA1. Ref.2

VAR_000389

Natural variant

298

1

A → T

VAR_000390

Natural variant

298

1

A → V

VAR_000391

Natural variant

305

1

S → L in GA1. Ref.12

VAR_000392

Natural variant

308

1

C → S in GA1.

VAR_000393

Natural variant

309

1

L → W in GA1.

VAR_000394

Natural variant

313

1

R → W in GA1.

VAR_000395

Natural variant

333

1

Q → E in GA1.

VAR_000396

Natural variant

349

1

A → T in GA1.

VAR_000397

Natural variant

354

1

G → R in GA1.

VAR_000398

Natural variant

354

1

G → S in GA1.

VAR_000399

Natural variant

355

1

R → C in GA1.

VAR_000400

Natural variant

355

1

R → H in GA1.

VAR_000401

Natural variant

365

1

E → K in GA1.

VAR_000402

Natural variant

375

1

C → R in GA1.

VAR_000403

Natural variant

382

1

A → T in GA1.

VAR_000404

Natural variant

383

1

R → C in GA1.

VAR_000405

Natural variant

383

1

R → H in GA1.

VAR_000406

Natural variant

386

1

R → Q in GA1.

VAR_000407

Natural variant

390

1

G → A in GA1. Ref.12

VAR_000409

Natural variant

390

1

G → R in GA1. Ref.12

VAR_000408

Natural variant

392

1

N → D in GA1.

VAR_000410

Natural variant

400

1

V → M in GA1.

VAR_000411

Natural variant

402

1

R → Q in GA1. Ref.13

VAR_000413

Natural variant

402

1

R → W in GA1; most common mutation identified; loss of tetramerization and enzyme activity. Ref.13

VAR_000412

Natural variant

403

1

H → R in GA1.

VAR_000414

Natural variant

406

1

N → K in GA1.

VAR_000415

Natural variant

407

1

L → P in GA1.

VAR_000416

Natural variant

414

1

E → K in GA1; loss of enzyme activity. Ref.13

VAR_000417

Natural variant

416

1

T → I in GA1. Ref.12

VAR_000418

Natural variant

421

1

A → T in GA1.

VAR_000419

Natural variant

421

1

A → V in GA1; impaired association of subunits.

VAR_000420

Natural variant

429

1

T → M in GA1.

VAR_000421

Natural variant

433

1

A → E in GA1.

VAR_000422

Experimental info

Mutagenesis

414

1

E → D: Reduced catalytic activity.

Sequence conflict

33

1

G → A in AAC52079. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

438

Helix Strand Turn

Details...

Helix

56 – 59

4

Helix

62 – 78

17

Helix

80 – 89

10

Helix

95 – 102

8

Helix

120 – 131

12

Helix

135 – 146

12

Helix

149 – 155

7

Helix

158 – 169

12

Beta strand

175 – 178

4

Beta strand

184 – 186

3

Helix

188 – 190

3

Beta strand

194 – 198

5

Turn

199 – 202

4

Beta strand

203 – 214

12

Helix

216 – 218

3

Beta strand

220 – 228

9

Beta strand

233 – 239

7

Beta strand

253 – 256

4

Beta strand

261 – 272

12

Helix

273 – 275

3

Helix

284 – 318

35

Helix

326 – 328

3

Helix

330 – 358

29

Helix

364 – 388

25

Helix

389 – 394

6

Helix

396 – 398

3

Helix

400 – 410

11

Beta strand

413 – 415

3

Helix

417 – 429

13

Sequences

	Sequence		Length	Mass (Da)
	Isoform Long [UniParc]. Last modified February 1, 1997. Version 1. Checksum: 415B8D510027BB63	FASTA	438	48,127
	10 20 30 40 50 60 MALRGVSVRL LSRGPGLHVL RTWVSSAAQT EKGGRTQSQL AKSSRPEFDW QDPLVLEEQL 70 80 90 100 110 120 TTDEILIRDT FRTYCQERLM PRILLANRNE VFHREIISEM GELGVLGPTI KGYGCAGVSS 130 140 150 160 170 180 VAYGLLAREL ERVDSGYRSA MSVQSSLVMH PIYAYGSEEQ RQKYLPQLAK GELLGCFGLT 190 200 210 220 230 240 EPNSGSDPSS METRAHYNSS NKSYTLNGTK TWITNSPMAD LFVVWARCED GCIRGFLLEK 250 260 270 280 290 300 GMRGLSAPRI QGKFSLRASA TGMIIMDGVE VPEENVLPGA SSLGGPFGCL NNARYGIAWG 310 320 330 340 350 360 VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD 370 380 390 400 410 420 KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHV IRHAMNLEAV NTYEGTHDIH 430 ALILGRAITG IQAFTASK
	Isoform Short. Checksum: 8E9E298E6DA9433C	FASTA	428	47,355
	10 20 30 40 50 60 MALRGVSVRL LSRGPGLHVL RTWVSSAAQT EKGGRTQSQL AKSSRPEFDW QDPLVLEEQL 70 80 90 100 110 120 TTDEILIRDT FRTYCQERLM PRILLANRNE VFHREIISEM GELGVLGPTI KGYGCAGVSS 130 140 150 160 170 180 VAYGLLAREL ERVDSGYRSA MSVQSSLVMH PIYAYGSEEQ RQKYLPQLAK GELLGCFGLT 190 200 210 220 230 240 EPNSGSDPSS METRAHYNSS NKSYTLNGTK TWITNSPMAD LFVVWARCED GCIRGFLLEK 250 260 270 280 290 300 GMRGLSAPRI QGKFSLRASA TGMIIMDGVE VPEENVLPGA SSLGGPFGCL NNARYGIAWG 310 320 330 340 350 360 VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD 370 380 390 400 410 420 KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHV IRHAMNLEAV NTYEVVQMCS LKRRWNSL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Pork and human cDNAs encoding glutaryl-CoA dehydrogenase." Goodman S.I., Kratz L.E., Frerman F.E. Prog. Clin. Biol. Res. 375:169-173(1992) [PubMed: 1438360] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM LONG). Tissue: Liver.
[2]	"Cloning of glutaryl-CoA dehydrogenase cDNA, and expression of wild type and mutant enzymes in Escherichia coli." Goodman S.I., Kratz L.E., Digiulio K.A., Biery B.J., Goodman K.E., Isaya G., Frerman F.E. Hum. Mol. Genet. 4:1493-1498(1995) [PubMed: 8541831] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS LONG AND SHORT), VARIANT GA1 HIS-295. Tissue: Liver.
[3]	"The human glutaryl-CoA dehydrogenase gene: report of intronic sequences and of 13 novel mutations causing glutaric aciduria type I." Schwartz M., Christensen E., Superti-Furga A., Brandt N.J. Hum. Genet. 102:452-458(1998) [PubMed: 9600243] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS GA1.
[4]	"Cloning of human full-length CDSs in BD Creator(TM) system donor vector." Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM LONG).
[5]	"The DNA sequence and biology of human chromosome 19." Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V. , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M. Nature 428:529-535(2004) [PubMed: 15057824] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM LONG). Tissue: Lymph.
[7]	"Glutaryl-CoA dehydrogenase mutations in glutaric acidemia (type I): review and report of thirty novel mutations." Goodman S.I., Stein D.E., Schlesinger S., Christensen E., Schwartz M., Greenberg C.R., Elpeleg O.N. Hum. Mutat. 12:141-144(1998) [PubMed: 9711871] [Abstract] Cited for: REVIEW ON VARIANTS.
[8]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[9]	"Crystal structures of human glutaryl-CoA dehydrogenase with and without an alternate substrate: structural bases of dehydrogenation and decarboxylation reactions." Fu Z., Wang M., Paschke R., Rao K.S., Frerman F.E., Kim J.-J.P. Biochemistry 43:9674-9684(2004) [PubMed: 15274622] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 47-438 IN COMPLEXES WITH SUBSTRATE ANALOG AND FAD, SUBUNIT.
[10]	"The effect of a Glu370Asp mutation in glutaryl-CoA dehydrogenase on proton transfer to the dienolate intermediate." Rao K.S., Fu Z., Albro M., Narayanan B., Baddam S., Lee H.-J.K., Kim J.-J.P., Frerman F.E. Biochemistry 46:14468-14477(2007) [PubMed: 18020372] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 45-438 OF MUTANT ASP-414 IN COMPLEXES WITH SUBSTRATE AND FAD.
[11]	"Gene structure and mutations of glutaryl-coenzyme A dehydrogenase: impaired association of enzyme subunits that is due to an A421V substitution causes glutaric acidemia type I in the Amish." Biery B.J., Stein D.E., Morton D.H., Goodman S.I. Am. J. Hum. Genet. 59:1006-1011(1996) [PubMed: 8900227] [Abstract] Cited for: VARIANTS GA1.
[12]	"Glutaric aciduria type I in the Arab and Jewish communities in Israel." Anikster Y., Shaag A., Joseph A., Mandel H., Ben-Zeev B., Christensen E., Elpeleg O.N. Am. J. Hum. Genet. 59:1012-1018(1996) [PubMed: 8900228] [Abstract] Cited for: VARIANTS GA1 ARG-101; PRO-283; THR-293; LEU-305; ARG-390 AND ILE-416.
[13]	"Disease-causing missense mutations affect enzymatic activity, stability and oligomerization of glutaryl-CoA dehydrogenase (GCDH)." Keyser B., Muehlhausen C., Dickmanns A., Christensen E., Muschol N., Ullrich K., Braulke T. Hum. Mol. Genet. 17:3854-3863(2008) [PubMed: 18775954] [Abstract] Cited for: CHARACTERIZATION OF VARIANTS GA1 GLY-138; TRP-402 AND LYS-414, SUBUNIT.
+	Additional computationally mapped references.

Web resources

GeneReviews

Cross-references

Sequence databases

EMBLGenBankDDBJ

U69141 mRNA. Translation: AAB08455.1.
AF012342 , AF012339, AF012340, AF012341 Genomic DNA. Translation: AAC52079.1.
BT006706 mRNA. Translation: AAP35352.1.
AD000092 Genomic DNA. Translation: AAB51174.1.
BC002579 mRNA. Translation: AAH02579.1.

IPI

IPI00024317.
IPI00218112.

PIR

T44260.
T45073.

RefSeq

NP_000150.1.
NP_039663.1.

UniGene

Hs.532699

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1SIQ	X-ray	2.10	A	47-438	[»]
1SIR	X-ray	2.60	A	45-438	[»]
2R0M	X-ray	2.70	A	45-438	[»]
2R0N	X-ray	2.30	A	45-438	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

Q92947. 2 interactions.

Proteomic databases

PRIDE

Q92947.

Genome annotation databases

Ensembl

ENSG00000105607. Homo sapiens. [Contig view]

GeneID

2639.

KEGG

hsa:2639.

NMPDR

fig|9606.3.peg.15791.

Organism-specific databases

GeneCards

GC19P012863.

H-InvDB

HIX0014810.

HGNC

HGNC:4189. GCDH.

MIM

231670. phenotype.
608801. gene.

Orphanet

25. Glutaryl-CoA dehydrogenase deficiency.

PharmGKB

PA28604.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

Q92947.

HOVERGEN

Q92947.

OMA

Q92947. KARYGIA.

Enzyme and pathway databases

BRENDA

1.3.99.7. 247.

Reactome

REACT_13. Metabolism of amino acids.

Gene expression databases

ArrayExpress

Q92947.

Bgee

Q92947.

CleanEx

HS_GCDH.

GermOnline

ENSG00000105607. Homo sapiens.

Family and domain databases

InterPro

IPR006089. Acyl-CoA_DH_CS.
IPR006092. Acyl-CoA_DH_N.
IPR006090. Acyl-CoA_Oxase/DH_1.
IPR006091. Acyl-CoA_Oxase/DH_M.
IPR013786. AcylCoA_DH/ox_N.
IPR013764. AcylCoA_oxidase/DH_1/2_C.
[Graphical view]

Gene3D

G3DSA:2.40.110.10. Acyl_CoA_DH/ox_M. 1 hit.
G3DSA:1.10.540.10. AcylCoA_DH/ox_N. 1 hit.
G3DSA:1.20.140.10. AcylCoA_DH_1/2_C. 1 hit.

Pfam

PF00441. Acyl-CoA_dh_1. 1 hit.
PF02770. Acyl-CoA_dh_M. 1 hit.
PF02771. Acyl-CoA_dh_N. 1 hit.
[Graphical view]

PROSITE

PS00072. ACYL_COA_DH_1. 1 hit.
PS00073. ACYL_COA_DH_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

10404.

SOURCE

Search...

Entry information

Entry name

GCDH_HUMAN

Accession

Primary (citable) accession number: Q92947
Secondary accession number(s): O14719

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	February 1, 1997
Last modified:	June 16, 2009
This is version 103 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)