• Gene id: 2731

Gene Summary

• Gene Symbol: GLDC   Gene   UCSC   Ensembl
• Aliases: GCE, GCSP, HYGN1
• Gene name: glycine decarboxylase
• Alternate names: glycine dehydrogenase (decarboxylating), mitochondrial, glycine cleavage system protein P, glycine decarboxylase P-protein, glycine dehydrogenase (aminomethyl-transferring), glycine dehydrogenase [decarboxylating], mitochondrial, nonketotic hyperglycinemia,
• Gene location: 9p24.1 (6645728: 6532466)     Exons: 25     NC_000009.12
• Gene summary(Entrez): Degradation of glycine is brought about by the glycine cleavage system, which is composed of four mitochondrial protein components: P protein (a pyridoxal phosphate-dependent glycine decarboxylase), H protein (a lipoic acid-containing protein), T protein
• OMIM: 238300

Protein Summary

• Protein general information: P23378  
  • Name: Glycine dehydrogenase (decarboxylating), mitochondrial (EC 1.4.4.2) (Glycine cleavage system P protein) (Glycine decarboxylase) (Glycine dehydrogenase (aminomethyl transferring))
  • Length: 1020  
  • Mass: 112730
• Sequence:

  MQSCARAWGLRLGRGVGGGRRLAGGSGPCWAPRSRDSSSGGGDSAAAGASRLLERLLPRHDDFARRHIGPGDKDQ
  REMLQTLGLASIDELIEKTVPANIRLKRPLKMEDPVCENEILATLHAISSKNQIWRSYIGMGYYNCSVPQTILRN
  LLENSGWITQYTPYQPEVSQGRLESLLNYQTMVCDITGLDMANASLLDEGTAAAEALQLCYRHNKRRKFLVDPRC
  HPQTIAVVQTRAKYTGVLTELKLPCEMDFSGKDVSGVLFQYPDTEGKVEDFTELVERAHQSGSLACCATDLLALC
  ILRPPGEFGVDIALGSSQRFGVPLGYGGPHAAFFAVRESLVRMMPGRMVGVTRDATGKEVYRLALQTREQHIRRD
  KATSNICTAQALLANMAAMFAIYHGSHGLEHIARRVHNATLILSEGLKRAGHQLQHDLFFDTLKIQCGCSVKEVL
  GRAAQRQINFRLFEDGTLGISLDETVNEKDLDDLLWIFGCESSAELVAESMGEECRGIPGSVFKRTSPFLTHQVF
  NSYHSETNIVRYMKKLENKDISLVHSMIPLGSCTMKLNSSSELAPITWKEFANIHPFVPLDQAQGYQQLFRELEK
  DLCELTGYDQVCFQPNSGAQGEYAGLATIRAYLNQKGEGHRTVCLIPKSAHGTNPASAHMAGMKIQPVEVDKYGN
  IDAVHLKAMVDKHKENLAAIMITYPSTNGVFEENISDVCDLIHQHGGQVYLDGANMNAQVGICRPGDFGSDVSHL
  NLHKTFCIPHGGGGPGMGPIGVKKHLAPFLPNHPVISLKRNEDACPVGTVSAAPWGSSSILPISWAYIKMMGGKG
  LKQATETAILNANYMAKRLETHYRILFRGARGYVGHEFILDTRPFKKSANIEAVDVAKRLQDYGFHAPTMSWPVA
  GTLMVEPTESEDKAELDRFCDAMISIRQEIADIEEGRIDPRVNPLKMSPHSLTCVTSSHWDRPYSREVAAFPLPF
  VKPENKFWPTIARIDDIYGDQHLVCTCPPMEVYESPFSEQKRASS

• Structural information:
  • Interpro: IPR001597  IPR003437  IPR020581  IPR015424  IPR015422   IPR015421  
  • CDD: cd00613
  • PDB: 6I33 6I34 6I35
  • PDBsum: 6I33 6I34 6I35
  • STRING: ENSP00000370737
• Other Databases: GeneCards:  GLDC  Malacards:  GLDC

Gene ontology

GO accession	Term name	Evidence code	Go category
GO:0005960	glycine cleavage complex	IBA	cellular component
GO:0016594	glycine binding	IBA	molecular function
GO:0030170	pyridoxal phosphate binding	IBA	molecular function
GO:0004375	glycine dehydrogenase (decarboxylating) activity	IBA	molecular function
GO:0005739	mitochondrion	IBA	cellular component
GO:0019464	glycine decarboxylation via glycine cleavage system	IBA	biological process
GO:0006546	glycine catabolic process	IDA	biological process
GO:0004375	glycine dehydrogenase (decarboxylating) activity	IDA	molecular function
GO:0005739	mitochondrion	IDA	cellular component
GO:0042803	protein homodimerization activity	ISS	molecular function
GO:0036255	response to methylamine	ISS	biological process
GO:1903442	response to lipoic acid	ISS	biological process
GO:0070280	pyridoxal binding	ISS	molecular function
GO:0006544	glycine metabolic process	IEA	biological process
GO:0006546	glycine catabolic process	IEA	biological process
GO:0016829	lyase activity	IEA	molecular function
GO:0055114	oxidation-reduction process	IEA	biological process
GO:0003824	catalytic activity	IEA	molecular function
GO:0004375	glycine dehydrogenase (decarboxylating) activity	IEA	molecular function
GO:0006520	cellular amino acid metabolic process	IEA	biological process
GO:0055114	oxidation-reduction process	IEA	biological process
GO:0016491	oxidoreductase activity	IEA	molecular function
GO:0005739	mitochondrion	IEA	cellular component
GO:0004375	glycine dehydrogenase (decarboxylating) activity	TAS	molecular function
GO:0006546	glycine catabolic process	TAS	biological process
GO:0004375	glycine dehydrogenase (decarboxylating) activity	IEA	molecular function
GO:0005759	mitochondrial matrix	TAS	cellular component
GO:0030170	pyridoxal phosphate binding	IEA	molecular function
GO:0016594	glycine binding	IEA	molecular function
GO:0005960	glycine cleavage complex	IEA	cellular component
GO:1990830	cellular response to leukemia inhibitory factor	IEA	biological process
GO:0065003	protein-containing complex assembly	IEA	biological process
GO:0019899	enzyme binding	IEA	molecular function
GO:0019464	glycine decarboxylation via glycine cleavage system	IEA	biological process
GO:0005739	mitochondrion	IEA	cellular component
GO:0004375	glycine dehydrogenase (decarboxylating) activity	IEA	molecular function
GO:0005739	mitochondrion	IEA	cellular component
GO:0005739	mitochondrion	IDA	cellular component
GO:0005654	nucleoplasm	IDA	cellular component
GO:0005886	plasma membrane	IDA	cellular component
GO:0022900	electron transport chain	IEA	biological process
GO:0009055	electron transfer activity	TAS	molecular function

KEGG pathways

Pathway id	Pathway name
hsa01100	Metabolic pathways
hsa01200	Carbon metabolism
hsa00260	Glycine, serine and threonine metabolism
hsa00630	Glyoxylate and dicarboxylate metabolism

Diseases

Associated diseases	References
Nonketotic hyperglycinemia	KEGG:H00191
Nonketotic hyperglycinemia	KEGG:H00191
Stomach cancer	PMID:26722042
Glycine encephalopathy	PMID:15851735
Aberrant CpGs in Low Motility Sperm	MIK: 21674046
Spermatogenic defects	MIK: 31037746
Teratozoospermia	MIK: 17327269

PubMed references

PMID	Condition	Mutation	Ethnicity	Population details	Infertility_type	Associated_genes
17327269	Teratozoospermia			13 (5 controls, 8 cases)	Male infertility	GSE6967 analyzed by GEO2R (cutoff 1.5 fold)
21674046	Aberrant CpGs in Low Motility Sperm			18	Male infertility	GSE26881
31037746	Spermatogenic defects			16 (1 control, 15 cases)	Male infertility	GSE6023 analyzed using GEO2R