GLDC

Functionⁱ

The glycine cleavage system catalyzes the degradation of glycine. The P protein (GLDC) binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO₂ is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein (GCSH).

3 Publications

Catalytic activityⁱ

glycine
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
+
H⁺
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
+
N⁶-lipoyl-L-lysyl-[glycine-cleavage complex H protein]
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
=
(R)-N⁶-(S⁸-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein]
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
+
CO₂
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
3 Publications
Manual assertion based on experiment inⁱ
- Ref.1
  "Structural and expression analyses of normal and mutant mRNA encoding glycine decarboxylase: three-base deletion in mRNA causes nonketotic hyperglycinemia."
  Kure S., Narisawa K., Tada K.
  Biochem. Biophys. Res. Commun. 174:1176-1182(1991) [PubMed] [Europe PMC] [Abstract]
  Cited for: NUCLEOTIDE SEQUENCE [MRNA], CATALYTIC ACTIVITY, VARIANT NKH PHE-756 DEL.
- Ref.2
  "The glycine cleavage system. Molecular cloning of the chicken and human glycine decarboxylase cDNAs and some characteristics involved in the deduced protein structures."
  Kume A., Koyata H., Sakakibara T., Ishiguro Y., Kure S., Hiraga K.
  J. Biol. Chem. 266:3323-3329(1991) [PubMed] [Europe PMC] [Abstract]
  Cited for: NUCLEOTIDE SEQUENCE [MRNA], CATALYTIC ACTIVITY.
- Ref.10
  "Nonketotic Hyperglycinemia: functional assessment of missense variants in GLDC to understand phenotypes of the disease."
  Bravo-Alonso I., Navarrete R., Arribas-Carreira L., Perona A., Abia D., Couce M.L., Garcia-Cazorla A., Morais A., Domingo R., Ramos M.A., Swanson M.A., Van Hove J.L., Ugarte M., Perez B., Perez-Cerda C., Rodriguez-Pombo P.
  Hum. Mutat. 38:678-691(2017) [PubMed] [Europe PMC] [Abstract]
  Cited for: FUNCTION, SUBCELLULAR LOCATION, CATALYTIC ACTIVITY, INVOLVEMENT IN NKH, VARIANTS NKH LYS-146; PRO-173; ALA-267; CYS-362; TRP-373; GLU-376; TRP-461; PRO-548; TYR-580; ARG-581; ASP-624; ASP-763; GLU-768; TRP-790; HIS-866; GLY-905; THR-933 AND ARG-994, CHARACTERIZATION OF VARIANTS NKH LYS-146; PRO-173; ALA-267; CYS-362; TRP-373; GLU-376; TRP-461; PRO-548; TYR-580; ARG-581; ASP-624; ASP-763; GLU-768; TRP-790; HIS-866; GLY-905; THR-933 AND ARG-994.
EC:
1.4.4.2
- Search proteins in UniProtKB for this EC number.
- See the description of this EC number in ENZYME.
- Search reactions for this EC number in Rhea.
3 Publications
Manual assertion based on experiment inⁱ
- Ref.1
  "Structural and expression analyses of normal and mutant mRNA encoding glycine decarboxylase: three-base deletion in mRNA causes nonketotic hyperglycinemia."
  Kure S., Narisawa K., Tada K.
  Biochem. Biophys. Res. Commun. 174:1176-1182(1991) [PubMed] [Europe PMC] [Abstract]
  Cited for: NUCLEOTIDE SEQUENCE [MRNA], CATALYTIC ACTIVITY, VARIANT NKH PHE-756 DEL.
- Ref.2
  "The glycine cleavage system. Molecular cloning of the chicken and human glycine decarboxylase cDNAs and some characteristics involved in the deduced protein structures."
  Kume A., Koyata H., Sakakibara T., Ishiguro Y., Kure S., Hiraga K.
  J. Biol. Chem. 266:3323-3329(1991) [PubMed] [Europe PMC] [Abstract]
  Cited for: NUCLEOTIDE SEQUENCE [MRNA], CATALYTIC ACTIVITY.
- Ref.10
  "Nonketotic Hyperglycinemia: functional assessment of missense variants in GLDC to understand phenotypes of the disease."
  Bravo-Alonso I., Navarrete R., Arribas-Carreira L., Perona A., Abia D., Couce M.L., Garcia-Cazorla A., Morais A., Domingo R., Ramos M.A., Swanson M.A., Van Hove J.L., Ugarte M., Perez B., Perez-Cerda C., Rodriguez-Pombo P.
  Hum. Mutat. 38:678-691(2017) [PubMed] [Europe PMC] [Abstract]
  Cited for: FUNCTION, SUBCELLULAR LOCATION, CATALYTIC ACTIVITY, INVOLVEMENT IN NKH, VARIANTS NKH LYS-146; PRO-173; ALA-267; CYS-362; TRP-373; GLU-376; TRP-461; PRO-548; TYR-580; ARG-581; ASP-624; ASP-763; GLU-768; TRP-790; HIS-866; GLY-905; THR-933 AND ARG-994, CHARACTERIZATION OF VARIANTS NKH LYS-146; PRO-173; ALA-267; CYS-362; TRP-373; GLU-376; TRP-461; PRO-548; TYR-580; ARG-581; ASP-624; ASP-763; GLU-768; TRP-790; HIS-866; GLY-905; THR-933 AND ARG-994.
Source:
Rhea
Search for this reaction in UniProtKB.
See the description of this reaction in Rhea.
. Show »« Hide
glycine
zoom
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H⁺
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N⁶-lipoyl-L-lysyl-[glycine-cleavage complex H protein]
(R)-N⁶-lipoyl-L-lysine residue
zoom
=
(R)-N⁶-(S⁸-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein]
(R)-N⁶-(S⁸-aminomethyldihydrolipoyl)-L-lysine residue
zoom
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CO₂

Cofactorⁱ

pyridoxal 5'-phosphateBy similarity

Activity regulationⁱ

Stimulated by lipoic acid. Inhibited in presence of methylamine (By similarity).By similarity

GO - Molecular functionⁱ

Complete GO annotation on QuickGO ...

GO - Biological processⁱ

Complete GO annotation on QuickGO ...

Keywordsⁱ

Molecular function	Oxidoreductase
Ligand	Pyridoxal phosphate

Enzyme and pathway databases

BioCycⁱ	MetaCyc:HS00622-MONOMER
BRENDAⁱ	1.4.4.2, 2681
PathwayCommonsⁱ	P23378
Reactomeⁱ	R-HSA-6783984, Glycine degradation
SABIO-RKⁱ	P23378

Names & Taxonomyⁱ

Protein namesⁱ	Recommended name: Glycine dehydrogenase (decarboxylating), mitochondrial1 Publication (EC:1.4.4.23 Publications) Alternative name(s): Glycine cleavage system P protein Glycine decarboxylase2 Publications Glycine dehydrogenase (aminomethyl-transferring)
Gene namesⁱ	Name:GLDCImported Synonyms:GCSPImported
Organismⁱ	Homo sapiens (Human)
Taxonomic identifierⁱ	9606 [NCBI]
Taxonomic lineageⁱ	cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Dipnotetrapodomorpha › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Boreoeutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo
Proteomesⁱ	UP000005640 Componentⁱ: Chromosome 9

Organism-specific databases

Human Gene Nomenclature Database More...HGNCⁱ	HGNC:4313, GLDC
MIMⁱ	238300, gene
neXtProtⁱ	NX_P23378
VEuPathDBⁱ	HostDB:ENSG00000178445.8

Keywords - Cellular componentⁱ

Mitochondrion

Pathology & Biotechⁱ

Involvement in diseaseⁱ

Non-ketotic hyperglycinemia (NKH)6 Publications

The disease is caused by variants affecting the gene represented in this entry.

Disease descriptionAutosomal recessive disease characterized by accumulation of a large amount of glycine in body fluid and by severe neurological symptoms.

Related information in OMIM

Feature key	Position(s)	DescriptionActions	Length
Natural variantⁱVAR_078776	146	T → K in NKH; loss of glycine catabolic process; loss of expression. 1 PublicationCorresponds to variant dbSNP:rs376578742EnsemblClinVar.	1
Natural variantⁱVAR_078777	173	L → P in NKH; loss of glycine catabolic process; decreased abundance. 1 Publication	1
Natural variantⁱVAR_078778	267	P → A in NKH; decreased glycine catabolic process; changed localization to the mitochondria; also expressed diffusely throughout the cytosol; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs1554648117EnsemblClinVar.	1
Natural variantⁱVAR_016849	283	A → P in NKH. 1 PublicationCorresponds to variant dbSNP:rs386833589EnsemblClinVar.	1
Natural variantⁱVAR_078779	362	R → C in NKH; decreased glycine catabolic process; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs10975674EnsemblClinVar.	1
Natural variantⁱVAR_078780	373	R → W in NKH; decreased glycine catabolic process; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs150171524EnsemblClinVar.	1
Natural variantⁱVAR_078781	376	K → E in NKH; decreased glycine catabolic process; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs774093619Ensembl.	1
Natural variantⁱVAR_078782	461	R → W in NKH; decreased glycine catabolic process; changed localization to the mitochondria; also expressed diffusely throughout the cytosol; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs761957837EnsemblClinVar.	1
Natural variantⁱVAR_016851	515	R → S in NKH. 1 PublicationCorresponds to variant dbSNP:rs121964976EnsemblClinVar.	1
Natural variantⁱVAR_078783	548	L → P in NKH; decreased GCS P-protein glycine exchange activity; no effect on abundance. 1 Publication	1
Natural variantⁱVAR_004979	564	S → I in NKH; common mutation in Finland. 1 PublicationCorresponds to variant dbSNP:rs121964974EnsemblClinVar.	1
Natural variantⁱVAR_078784	580	H → Y in NKH; loss of glycine catabolic process; loss of expression. 1 Publication	1
Natural variantⁱVAR_078785	581	P → R in NKH; loss of glycine catabolic process; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs772871471EnsemblClinVar.	1
Natural variantⁱVAR_078786	624	A → D in NKH; loss of GCS P-protein glycine exchange activity; no effect on abundance. 1 Publication	1
Natural variantⁱVAR_009939	756	Missing in NKH. 1 Publication	1
Natural variantⁱVAR_078787	763	G → D in NKH; loss of GCS P-protein glycine exchange activity; no effect on abundance. 1 PublicationCorresponds to variant dbSNP:rs1374110692Ensembl.	1
Natural variantⁱVAR_078788	768	G → E in NKH; loss of GCS P-protein glycine exchange activity; no effect on abundance. 1 Publication	1
Natural variantⁱVAR_078789	790	R → W in NKH; decreased glycine catabolic process; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs386833556EnsemblClinVar.	1
Natural variantⁱVAR_079313	839	Y → C in NKH. 1 Publication	1
Natural variantⁱVAR_078790	866	D → H in NKH; decreased glycine catabolic process; decreased abundance. 1 Publication	1
Natural variantⁱVAR_078791	905	V → G in NKH; decreased GCS P-protein glycine exchange activity; no effect on abundance. 1 PublicationCorresponds to variant dbSNP:rs188269735EnsemblClinVar.	1
Natural variantⁱVAR_078792	933	I → T in NKH; decreased glycine catabolic process; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs758029533EnsemblClinVar.	1
Natural variantⁱVAR_078793	994	G → R in NKH; loss of glycine catabolic process; loss of expression. 1 PublicationCorresponds to variant dbSNP:rs1406713104EnsemblClinVar.	1

Keywords - Diseaseⁱ

Disease variant

Organism-specific databases

DisGeNET More...DisGeNETⁱ	2731
GeneReviewsⁱ	GLDC
MalaCards human disease database More...MalaCardsⁱ	GLDC
MIMⁱ	605899, phenotype
Open Targets More...OpenTargetsⁱ	ENSG00000178445
Orphanetⁱ	289863, Atypical glycine encephalopathy 289860, Infantile glycine encephalopathy 289857, Neonatal glycine encephalopathy
PharmGKBⁱ	PA28716

Miscellaneous databases

Pharosⁱ	P23378, Tbio

Pharosⁱ

P23378, Tbio

Chemistry databases

Drug and drug target database More...DrugBankⁱ	DB00145, Glycine DB00114, Pyridoxal phosphate

DrugBankⁱ

DB00145, Glycine
DB00114, Pyridoxal phosphate

Genetic variation databases

BioMutaⁱ	GLDC
DMDMⁱ	229462870

PTM / Processingⁱ

Molecule processing

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Transit peptideⁱ	1 – 35	MitochondrionSequence analysisAdd BLAST		35
ChainⁱPRO_0000010740	36 – 1020	Glycine dehydrogenase (decarboxylating), mitochondrialAdd BLAST		985

Amino acid modifications

Feature key	Position(s)	DescriptionActions	Length
Modified residueⁱ	447	N6-acetyllysineBy similarity	1
Modified residueⁱ	514	N6-acetyllysineBy similarity	1
Modified residueⁱ	648	N6-acetyllysineBy similarity	1
Modified residueⁱ	664	N6-acetyllysineBy similarity	1
Modified residueⁱ	754	N6-(pyridoxal phosphate)lysineBy similarity	1

Keywords - PTMⁱ

Acetylation

Proteomic databases

EPDⁱ	P23378
jPOSTⁱ	P23378
MassIVEⁱ	P23378
MaxQB - The MaxQuant DataBase More...MaxQBⁱ	P23378
PaxDbⁱ	P23378
PeptideAtlas More...PeptideAtlasⁱ	P23378
PRIDEⁱ	P23378
ProteomicsDBⁱ	54084

PTM databases

iPTMnetⁱ	P23378
PhosphoSitePlusⁱ	P23378

Expressionⁱ

Gene expression databases

Bgeeⁱ	ENSG00000178445, Expressed in placenta and 179 other tissues
ExpressionAtlasⁱ	P23378, baseline and differential
Genevisibleⁱ	P23378, HS

Organism-specific databases

Human Protein Atlas More...HPAⁱ	ENSG00000178445, Group enriched (kidney, liver, placenta)

HPAⁱ

ENSG00000178445, Group enriched (kidney, liver, placenta)

Interactionⁱ

Subunit structureⁱ

Homodimer (By similarity).

Interacts with GCSH (By similarity). The glycine cleavage system is composed of four proteins: P (GLDC), T (GCST), L (DLD) and H (GCSH).

By similarity

GO - Molecular functionⁱ

enzyme binding Source: Ensembl
protein homodimerization activity Source: UniProtKB

Complete GO annotation on QuickGO ...

Protein-protein interaction databases

BioGRIDⁱ	108993, 24 interactors
IntActⁱ	P23378, 17 interactors
Molecular INTeraction database More...MINTⁱ	P23378
STRINGⁱ	9606.ENSP00000370737

Miscellaneous databases

RNActⁱ	P23378, protein

RNActⁱ

P23378, protein

Structureⁱ

Secondary structure

Legend: HelixTurnBeta strandPDB Structure known for this area

Feature key	Position(s)	DescriptionActions	Length
Helixⁱ	52 – 56	Combined sources	5
Helixⁱ	64 – 67	Combined sources	4
Helixⁱ	72 – 81	Combined sources	10
Helixⁱ	87 – 94	Combined sources	8
Helixⁱ	97 – 99	Combined sources	3
Helixⁱ	113 – 124	Combined sources	12
Helixⁱ	145 – 150	Combined sources	6
Turnⁱ	151 – 153	Combined sources	3
Helixⁱ	155 – 158	Combined sources	4
Helixⁱ	166 – 168	Combined sources	3
Helixⁱ	170 – 187	Combined sources	18
Beta strandⁱ	190 – 192	Combined sources	3
Helixⁱ	199 – 214	Combined sources	16
Beta strandⁱ	217 – 221	Combined sources	5
Helixⁱ	227 – 240	Combined sources	14
Beta strandⁱ	243 – 246	Combined sources	4
Helixⁱ	249 – 251	Combined sources	3
Beta strandⁱ	259 – 267	Combined sources	9
Helixⁱ	277 – 285	Combined sources	9
Beta strandⁱ	289 – 294	Combined sources	6
Helixⁱ	298 – 300	Combined sources	3
Helixⁱ	305 – 308	Combined sources	4
Beta strandⁱ	311 – 316	Combined sources	6
Turnⁱ	318 – 321	Combined sources	4
Helixⁱ	325 – 327	Combined sources	3
Beta strandⁱ	332 – 336	Combined sources	5
Helixⁱ	338 – 343	Combined sources	6
Beta strandⁱ	349 – 354	Combined sources	6
Beta strandⁱ	359 – 363	Combined sources	5
Helixⁱ	366 – 368	Combined sources	3
Helixⁱ	370 – 373	Combined sources	4
Helixⁱ	374 – 376	Combined sources	3
Helixⁱ	386 – 424	Combined sources	39
Beta strandⁱ	428 – 430	Combined sources	3
Beta strandⁱ	432 – 441	Combined sources	10
Helixⁱ	446 – 455	Combined sources	10
Beta strandⁱ	468 – 471	Combined sources	4
Helixⁱ	478 – 487	Combined sources	10
Helixⁱ	494 – 500	Combined sources	7
Helixⁱ	508 – 510	Combined sources	3
Helixⁱ	523 – 526	Combined sources	4
Helixⁱ	531 – 543	Combined sources	13
Turnⁱ	548 – 550	Combined sources	3
Turnⁱ	556 – 558	Combined sources	3
Helixⁱ	565 – 568	Combined sources	4
Helixⁱ	569 – 572	Combined sources	4
Helixⁱ	574 – 577	Combined sources	4
Helixⁱ	585 – 587	Combined sources	3
Helixⁱ	589 – 606	Combined sources	18
Beta strandⁱ	609 – 612	Combined sources	4
Helixⁱ	618 – 635	Combined sources	18
Beta strandⁱ	643 – 647	Combined sources	5
Helixⁱ	653 – 660	Combined sources	8
Beta strandⁱ	664 – 668	Combined sources	5
Beta strandⁱ	674 – 676	Combined sources	3
Helixⁱ	678 – 688	Combined sources	11
Turnⁱ	689 – 691	Combined sources	3
Beta strandⁱ	692 – 700	Combined sources	9
Helixⁱ	710 – 718	Combined sources	9
Turnⁱ	719 – 721	Combined sources	3
Beta strandⁱ	723 – 727	Combined sources	5
Helixⁱ	728 – 733	Combined sources	6
Turnⁱ	734 – 737	Combined sources	4
Helixⁱ	740 – 742	Combined sources	3
Beta strandⁱ	746 – 749	Combined sources	4
Helixⁱ	752 – 755	Combined sources	4
Turnⁱ	761 – 763	Combined sources	3
Beta strandⁱ	770 – 772	Combined sources	3
Helixⁱ	774 – 779	Combined sources	6
Beta strandⁱ	784 – 786	Combined sources	3
Beta strandⁱ	791 – 793	Combined sources	3
Beta strandⁱ	801 – 803	Combined sources	3
Helixⁱ	808 – 810	Combined sources	3
Helixⁱ	811 – 844	Combined sources	34
Turnⁱ	845 – 847	Combined sources	3
Beta strandⁱ	848 – 850	Combined sources	3
Beta strandⁱ	863 – 866	Combined sources	4
Helixⁱ	869 – 874	Combined sources	6
Helixⁱ	878 – 887	Combined sources	10
Beta strandⁱ	893 – 896	Combined sources	4
Beta strandⁱ	903 – 905	Combined sources	3
Helixⁱ	913 – 934	Combined sources	22
Beta strandⁱ	940 – 943	Combined sources	4
Helixⁱ	944 – 947	Combined sources	4
Helixⁱ	952 – 956	Combined sources	5
Helixⁱ	966 – 970	Combined sources	5
Helixⁱ	978 – 980	Combined sources	3
Beta strandⁱ	985 – 987	Combined sources	3
Helixⁱ	991 – 996	Combined sources	6

Show more details

3D structure databases

SMRⁱ	P23378
ModBaseⁱ	Search...
PDBe-KBⁱ	Search...

Family & Domainsⁱ

Region

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Regionⁱ	21 – 46	DisorderedSequence analysisAdd BLAST		26

Sequence similaritiesⁱ

Belongs to the GcvP family.Curated

Keywords - Domainⁱ

Transit peptide

Phylogenomic databases

eggNOGⁱ	KOG2040, Eukaryota
Ensembl GeneTree More...GeneTreeⁱ	ENSGT00390000017970
HOGENOMⁱ	CLU_004620_3_2_1
InParanoidⁱ	P23378
OMAⁱ	CVPMSEY
Database of Orthologous Groups More...OrthoDBⁱ	390348at2759
PhylomeDBⁱ	P23378
TreeFamⁱ	TF300678

Family and domain databases

Conserved Domains Database More...CDDⁱ	cd00613, GDC-P, 2 hits
Gene3Dⁱ	3.40.640.10, 2 hits 3.90.1150.10, 1 hit
HAMAPⁱ	MF_00711, GcvP, 1 hit
InterProⁱ	View protein in InterPro IPR001597, ArAA_b-elim_lyase/Thr_aldolase IPR003437, GcvP IPR020581, GDC_P IPR015424, PyrdxlP-dep_Trfase IPR015422, PyrdxlP-dep_Trfase_dom1 IPR015421, PyrdxlP-dep_Trfase_major
PANTHERⁱ	PTHR11773, PTHR11773, 1 hit
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF01212, Beta_elim_lyase, 1 hit PF02347, GDC-P, 1 hit
SUPFAMⁱ	SSF53383, SSF53383, 2 hits
TIGRFAMsⁱ	TIGR00461, gcvP, 1 hit

Sequence (1+)ⁱ

Sequence statusⁱ: Complete.

Sequence processingⁱ: The displayed sequence is further processed into a mature form.

This entry has 1 described isoform and 9 potential isoforms that are computationally mapped.Show all Align All

P23378-1 [UniParc]FASTA Add to basket

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        10         20         30         40         50
MQSCARAWGL RLGRGVGGGR RLAGGSGPCW APRSRDSSSG GGDSAAAGAS 
        60         70         80         90        100
RLLERLLPRH DDFARRHIGP GDKDQREMLQ TLGLASIDEL IEKTVPANIR 
       110        120        130        140        150
LKRPLKMEDP VCENEILATL HAISSKNQIW RSYIGMGYYN CSVPQTILRN 
       160        170        180        190        200
LLENSGWITQ YTPYQPEVSQ GRLESLLNYQ TMVCDITGLD MANASLLDEG 
       210        220        230        240        250
TAAAEALQLC YRHNKRRKFL VDPRCHPQTI AVVQTRAKYT GVLTELKLPC 
       260        270        280        290        300
EMDFSGKDVS GVLFQYPDTE GKVEDFTELV ERAHQSGSLA CCATDLLALC 
       310        320        330        340        350
ILRPPGEFGV DIALGSSQRF GVPLGYGGPH AAFFAVRESL VRMMPGRMVG 
       360        370        380        390        400
VTRDATGKEV YRLALQTREQ HIRRDKATSN ICTAQALLAN MAAMFAIYHG 
       410        420        430        440        450
SHGLEHIARR VHNATLILSE GLKRAGHQLQ HDLFFDTLKI QCGCSVKEVL 
       460        470        480        490        500
GRAAQRQINF RLFEDGTLGI SLDETVNEKD LDDLLWIFGC ESSAELVAES 
       510        520        530        540        550
MGEECRGIPG SVFKRTSPFL THQVFNSYHS ETNIVRYMKK LENKDISLVH 
       560        570        580        590        600
SMIPLGSCTM KLNSSSELAP ITWKEFANIH PFVPLDQAQG YQQLFRELEK 
       610        620        630        640        650
DLCELTGYDQ VCFQPNSGAQ GEYAGLATIR AYLNQKGEGH RTVCLIPKSA 
       660        670        680        690        700
HGTNPASAHM AGMKIQPVEV DKYGNIDAVH LKAMVDKHKE NLAAIMITYP 
       710        720        730        740        750
STNGVFEENI SDVCDLIHQH GGQVYLDGAN MNAQVGICRP GDFGSDVSHL 
       760        770        780        790        800
NLHKTFCIPH GGGGPGMGPI GVKKHLAPFL PNHPVISLKR NEDACPVGTV 
       810        820        830        840        850
SAAPWGSSSI LPISWAYIKM MGGKGLKQAT ETAILNANYM AKRLETHYRI 
       860        870        880        890        900
LFRGARGYVG HEFILDTRPF KKSANIEAVD VAKRLQDYGF HAPTMSWPVA 
       910        920        930        940        950
GTLMVEPTES EDKAELDRFC DAMISIRQEI ADIEEGRIDP RVNPLKMSPH 
       960        970        980        990       1000
SLTCVTSSHW DRPYSREVAA FPLPFVKPEN KFWPTIARID DIYGDQHLVC 
      1010       1020
TCPPMEVYES PFSEQKRASS

Length:1,020

Mass (Da):112,730

Last modified:May 5, 2009 - v2

Checksum:ⁱ8FAEA7D56BEB17B2

GO

Computationally mapped potential isoform sequencesⁱ

There are 9 potential isoforms mapped to this entry.BLAST Align Show all Add to basket

Entry	Entry name	Protein names	Gene names	Length	Annotation

A0A1W2PP74	A0A1W2PP74_HUMAN	Glycine dehydrogenase (aminomethyl-... Glycine dehydrogenase (aminomethyl-transferring), EC 1.4.4.2	GLDC	420	Annotation score:
A0A1W2PQV3	A0A1W2PQV3_HUMAN	Glycine dehydrogenase (aminomethyl-... Glycine dehydrogenase (aminomethyl-transferring), EC 1.4.4.2	GLDC	388	Annotation score:
A0A1W2PPB1	A0A1W2PPB1_HUMAN	Glycine dehydrogenase (decarboxylat... Glycine dehydrogenase (decarboxylating), mitochondrial	GLDC	254	Annotation score:
A0A1W2PPE1	A0A1W2PPE1_HUMAN	Glycine dehydrogenase (decarboxylat... Glycine dehydrogenase (decarboxylating), mitochondrial	GLDC	164	Annotation score:
A0A1W2PPG0	A0A1W2PPG0_HUMAN	Glycine dehydrogenase (decarboxylat... Glycine dehydrogenase (decarboxylating), mitochondrial	GLDC	55	Annotation score:
A0A1W2PPH6	A0A1W2PPH6_HUMAN	Glycine dehydrogenase (decarboxylat... Glycine dehydrogenase (decarboxylating), mitochondrial	GLDC	140	Annotation score:
A0A1W2PQU6	A0A1W2PQU6_HUMAN	Glycine dehydrogenase (decarboxylat... Glycine dehydrogenase (decarboxylating), mitochondrial	GLDC	106	Annotation score:
A0A1W2PPK8	A0A1W2PPK8_HUMAN	Glycine dehydrogenase (decarboxylat... Glycine dehydrogenase (decarboxylating), mitochondrial	GLDC	103	Annotation score:
A0A1W2PPD7	A0A1W2PPD7_HUMAN	Glycine dehydrogenase (decarboxylat... Glycine dehydrogenase (decarboxylating), mitochondrial	GLDC	64	Annotation score:

Experimental Info

Feature key	Position(s)	DescriptionActions	Length
Sequence conflictⁱ	396	A → R in AAA36463 (PubMed:1993704).Curated	1
Sequence conflictⁱ	396	A → R in BAA14286 (PubMed:1993704).Curated	1
Sequence conflictⁱ	441	Q → H in AAA36478 (PubMed:1996985).Curated	1
Sequence conflictⁱ	441	Q → H in AAA36463 (PubMed:1993704).Curated	1
Sequence conflictⁱ	441	Q → H in BAA14286 (PubMed:1993704).Curated	1
Sequence conflictⁱ	608	Y → H in AAA36478 (PubMed:1996985).Curated	1
Sequence conflictⁱ	976	V → M in AAA36463 (PubMed:1993704).Curated	1
Sequence conflictⁱ	976	V → M in BAA14286 (PubMed:1993704).Curated	1

Natural variant

Feature key	Position(s)	DescriptionActions	Length
Natural variantⁱVAR_078776	146	T → K in NKH; loss of glycine catabolic process; loss of expression. 1 PublicationCorresponds to variant dbSNP:rs376578742EnsemblClinVar.	1
Natural variantⁱVAR_078777	173	L → P in NKH; loss of glycine catabolic process; decreased abundance. 1 Publication	1
Natural variantⁱVAR_078778	267	P → A in NKH; decreased glycine catabolic process; changed localization to the mitochondria; also expressed diffusely throughout the cytosol; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs1554648117EnsemblClinVar.	1
Natural variantⁱVAR_016849	283	A → P in NKH. 1 PublicationCorresponds to variant dbSNP:rs386833589EnsemblClinVar.	1
Natural variantⁱVAR_016850	329	P → T in one non-ketotic hyperglycinemia patient. 1 PublicationCorresponds to variant dbSNP:rs386833593EnsemblClinVar.	1
Natural variantⁱVAR_078779	362	R → C in NKH; decreased glycine catabolic process; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs10975674EnsemblClinVar.	1
Natural variantⁱVAR_078780	373	R → W in NKH; decreased glycine catabolic process; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs150171524EnsemblClinVar.	1
Natural variantⁱVAR_078781	376	K → E in NKH; decreased glycine catabolic process; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs774093619Ensembl.	1
Natural variantⁱVAR_078782	461	R → W in NKH; decreased glycine catabolic process; changed localization to the mitochondria; also expressed diffusely throughout the cytosol; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs761957837EnsemblClinVar.	1
Natural variantⁱVAR_016851	515	R → S in NKH. 1 PublicationCorresponds to variant dbSNP:rs121964976EnsemblClinVar.	1
Natural variantⁱVAR_078783	548	L → P in NKH; decreased GCS P-protein glycine exchange activity; no effect on abundance. 1 Publication	1
Natural variantⁱVAR_004979	564	S → I in NKH; common mutation in Finland. 1 PublicationCorresponds to variant dbSNP:rs121964974EnsemblClinVar.	1
Natural variantⁱVAR_078784	580	H → Y in NKH; loss of glycine catabolic process; loss of expression. 1 Publication	1
Natural variantⁱVAR_078785	581	P → R in NKH; loss of glycine catabolic process; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs772871471EnsemblClinVar.	1
Natural variantⁱVAR_078786	624	A → D in NKH; loss of GCS P-protein glycine exchange activity; no effect on abundance. 1 Publication	1
Natural variantⁱVAR_009939	756	Missing in NKH. 1 Publication	1
Natural variantⁱVAR_078787	763	G → D in NKH; loss of GCS P-protein glycine exchange activity; no effect on abundance. 1 PublicationCorresponds to variant dbSNP:rs1374110692Ensembl.	1
Natural variantⁱVAR_078788	768	G → E in NKH; loss of GCS P-protein glycine exchange activity; no effect on abundance. 1 Publication	1
Natural variantⁱVAR_078789	790	R → W in NKH; decreased glycine catabolic process; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs386833556EnsemblClinVar.	1
Natural variantⁱVAR_079313	839	Y → C in NKH. 1 Publication	1
Natural variantⁱVAR_078790	866	D → H in NKH; decreased glycine catabolic process; decreased abundance. 1 Publication	1
Natural variantⁱVAR_078791	905	V → G in NKH; decreased GCS P-protein glycine exchange activity; no effect on abundance. 1 PublicationCorresponds to variant dbSNP:rs188269735EnsemblClinVar.	1
Natural variantⁱVAR_078792	933	I → T in NKH; decreased glycine catabolic process; decreased abundance. 1 PublicationCorresponds to variant dbSNP:rs758029533EnsemblClinVar.	1
Natural variantⁱVAR_078793	994	G → R in NKH; loss of glycine catabolic process; loss of expression. 1 PublicationCorresponds to variant dbSNP:rs1406713104EnsemblClinVar.	1

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	M63635 mRNA Translation: AAA36478.1 M64590 mRNA Translation: AAA36463.1 D90239 mRNA Translation: BAA14286.1 AK314156 mRNA Translation: BAG36841.1 AL353718 Genomic DNA No translation available. AL162411 Genomic DNA No translation available. CH471071 Genomic DNA Translation: EAW58740.1 BC111993 mRNA Translation: AAI11994.1 BC111995 mRNA Translation: AAI11996.1
The Consensus CDS (CCDS) project More...CCDSⁱ	CCDS34987.1
PIRⁱ	JN0124
NCBI Reference Sequences More...RefSeqⁱ	NP_000161.2, NM_000170.2

Genome annotation databases

Ensemblⁱ	ENST00000321612; ENSP00000370737; ENSG00000178445
GeneIDⁱ	2731
KEGGⁱ	hsa:2731
UCSC genome browser More...UCSCⁱ	uc003zkc.4, human

Similar proteinsⁱ

100% Identity
90% Identity
50% Identity

Protein	Similar proteins		Species	Score	Length	Source
P23378	Glycine dehydrogenase (decarboxylating), mitochondrial		HUMAN		254	UniRef100_P23378
Glycine dehydrogenase (decarboxylating), mitochondrial (Fragment)		HUMAN		164

Protein	Similar proteins		Species	Score	Length	Source
P23378	Glycine dehydrogenase (decarboxylating), mitochondrial		HUMAN		254	UniRef90_P23378
Glycine cleavage system P protein		PAPAN		987
Glycine cleavage system P protein		NOMLE		914
Glycine cleavage system P protein		PANPA		914
Glycine cleavage system P protein		PANTR		914
+8

Protein	Similar proteins		Species	Score	Length	Source
P23378	Glycine dehydrogenase (decarboxylating), mitochondrial		CHICK		1004	UniRef50_P23378
Glycine dehydrogenase (decarboxylating), mitochondrial		HUMAN		254
Glycine cleavage system P protein		PAPAN		987
Glycine cleavage system P protein		PANPA		914
Glycine cleavage system P protein		GORGO		914
+486

Cross-referencesⁱ

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	M63635 mRNA Translation: AAA36478.1 M64590 mRNA Translation: AAA36463.1 D90239 mRNA Translation: BAA14286.1 AK314156 mRNA Translation: BAG36841.1 AL353718 Genomic DNA No translation available. AL162411 Genomic DNA No translation available. CH471071 Genomic DNA Translation: EAW58740.1 BC111993 mRNA Translation: AAI11994.1 BC111995 mRNA Translation: AAI11996.1
CCDSⁱ	CCDS34987.1
PIRⁱ	JN0124
RefSeqⁱ	NP_000161.2, NM_000170.2

3D structure databases

Select the link destinations: Protein Data Bank Europe More...PDBeⁱ Protein Data Bank RCSB More...RCSB PDBⁱ Protein Data Bank Japan More...PDBjⁱ Links Updated	PDB entry	Method	Resolution (Å)	Chain	Positions	PDBsum
	6I33	X-ray	2.30	A/B	45-1020	[»]
	6I34	X-ray	2.10	A/B/C/D	45-1020	[»]
	6I35	X-ray	2.00	A/B/C/D	45-1020	[»]
SMRⁱ	P23378
ModBaseⁱ	Search...
PDBe-KBⁱ	Search...

Protein-protein interaction databases

BioGRIDⁱ	108993, 24 interactors
IntActⁱ	P23378, 17 interactors
MINTⁱ	P23378
STRINGⁱ	9606.ENSP00000370737

Chemistry databases

DrugBankⁱ	DB00145, Glycine DB00114, Pyridoxal phosphate

DrugBankⁱ

DB00145, Glycine
DB00114, Pyridoxal phosphate

PTM databases

iPTMnetⁱ	P23378
PhosphoSitePlusⁱ	P23378

Genetic variation databases

BioMutaⁱ	GLDC
DMDMⁱ	229462870

Proteomic databases

EPDⁱ	P23378
jPOSTⁱ	P23378
MassIVEⁱ	P23378
MaxQBⁱ	P23378
PaxDbⁱ	P23378
PeptideAtlasⁱ	P23378
PRIDEⁱ	P23378
ProteomicsDBⁱ	54084

Protocols and materials databases

Antibodypediaⁱ	9715, 195 antibodies
The DNASU plasmid repository More...DNASUⁱ	2731

Genome annotation databases

Ensemblⁱ	ENST00000321612; ENSP00000370737; ENSG00000178445
GeneIDⁱ	2731
KEGGⁱ	hsa:2731
UCSCⁱ	uc003zkc.4, human

Organism-specific databases

CTDⁱ	2731
DisGeNETⁱ	2731
GeneCardsⁱ	GLDC
GeneReviewsⁱ	GLDC
HGNCⁱ	HGNC:4313, GLDC
HPAⁱ	ENSG00000178445, Group enriched (kidney, liver, placenta)
MalaCardsⁱ	GLDC
MIMⁱ	238300, gene 605899, phenotype
neXtProtⁱ	NX_P23378
OpenTargetsⁱ	ENSG00000178445
Orphanetⁱ	289863, Atypical glycine encephalopathy 289860, Infantile glycine encephalopathy 289857, Neonatal glycine encephalopathy
PharmGKBⁱ	PA28716
VEuPathDBⁱ	HostDB:ENSG00000178445.8
GenAtlas: human gene database More...GenAtlasⁱ	Search...

Phylogenomic databases

eggNOGⁱ	KOG2040, Eukaryota
GeneTreeⁱ	ENSGT00390000017970
HOGENOMⁱ	CLU_004620_3_2_1
InParanoidⁱ	P23378
OMAⁱ	CVPMSEY
OrthoDBⁱ	390348at2759
PhylomeDBⁱ	P23378
TreeFamⁱ	TF300678

Enzyme and pathway databases

BioCycⁱ	MetaCyc:HS00622-MONOMER
BRENDAⁱ	1.4.4.2, 2681
PathwayCommonsⁱ	P23378
Reactomeⁱ	R-HSA-6783984, Glycine degradation
SABIO-RKⁱ	P23378

Miscellaneous databases

BioGRID-ORCSⁱ	2731, 6 hits in 988 CRISPR screens
ChiTaRSⁱ	GLDC, human
GeneWikiⁱ	Glycine_dehydrogenase_(decarboxylating)
GenomeRNAiⁱ	2731
Pharosⁱ	P23378, Tbio
Protein Ontology More...PROⁱ	PR:P23378
RNActⁱ	P23378, protein
SOURCEⁱ	Search...

Gene expression databases

Bgeeⁱ	ENSG00000178445, Expressed in placenta and 179 other tissues
ExpressionAtlasⁱ	P23378, baseline and differential
Genevisibleⁱ	P23378, HS

Family and domain databases

CDDⁱ	cd00613, GDC-P, 2 hits
Gene3Dⁱ	3.40.640.10, 2 hits 3.90.1150.10, 1 hit
HAMAPⁱ	MF_00711, GcvP, 1 hit
InterProⁱ	View protein in InterPro IPR001597, ArAA_b-elim_lyase/Thr_aldolase IPR003437, GcvP IPR020581, GDC_P IPR015424, PyrdxlP-dep_Trfase IPR015422, PyrdxlP-dep_Trfase_dom1 IPR015421, PyrdxlP-dep_Trfase_major
PANTHERⁱ	PTHR11773, PTHR11773, 1 hit
Pfamⁱ	View protein in Pfam PF01212, Beta_elim_lyase, 1 hit PF02347, GDC-P, 1 hit
SUPFAMⁱ	SSF53383, SSF53383, 2 hits
TIGRFAMsⁱ	TIGR00461, gcvP, 1 hit
MobiDBⁱ	Search...

Entry informationⁱ

Entry nameⁱ	GCSP_HUMAN
Accessionⁱ	P23378Primary (citable) accession number: P23378 Secondary accession number(s): Q2M2F8
Entry historyⁱ	Integrated into UniProtKB/Swiss-Prot:	November 1, 1991
	Last sequence update:	May 5, 2009
	Last modified:	June 2, 2021
	This is version 187 of the entry and version 2 of the sequence. See complete history.
Entry statusⁱ	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.

Miscellaneousⁱ

Keywords - Technical termⁱ

3D-structure, Reference proteome

Documents

Human chromosome 9
Human chromosome 9: entries, gene names and cross-references to MIM
Human entries with genetic variants
List of human entries with genetic variants
Human variants curated from literature reports
Index of human variants curated from literature reports
MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
PDB cross-references
Index of Protein Data Bank (PDB) cross-references
SIMILARITY comments
Index of protein domains and families

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Glycine dehydrogenase (decarboxylating), mitochondrial

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Functionⁱ

Catalytic activityⁱ

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

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Keywords - Cellular componentⁱ

Pathology & Biotechⁱ

Keywords - Diseaseⁱ

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Keywords - PTMⁱ

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GO - Molecular functionⁱ

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Keywords - Domainⁱ

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