MultifacetedProtDB - Bologna Biocomputing Group

EC number	EC number description
2.1.2.1	Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases; glycine hydroxymethyltransferase

Structure

PDB	Resolution (Å)	PDB name
1BJ4	2.65	RECOMBINANT SERINE HYDROXYMETHYLTRANSFERASE (HUMAN)
6FL5	3.6	Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution
6M5W	3.1	Co-crystal structure of human serine hydroxymethyltransferase 1 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid
7RJL	1.5	Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT
7RJP	1.25	Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with SHMT

GO term

GO ontology	GO term	GO description
Biological Process	GO:0006565	L-serine catabolic process
Biological Process	GO:0006563	L-serine metabolic process
Biological Process	GO:1990830	cellular response to leukemia inhibitory factor
Biological Process	GO:1904482	cellular response to tetrahydrofolate
Biological Process	GO:0006231	dTMP biosynthetic process
Biological Process	GO:0046655	folic acid metabolic process
Biological Process	GO:0019264	glycine biosynthetic process from serine
Biological Process	GO:0006544	glycine metabolic process
Biological Process	GO:0017148	negative regulation of translation
Biological Process	GO:0051289	protein homotetramerization
Biological Process	GO:0009113	purine nucleobase biosynthetic process
Biological Process	GO:0035999	tetrahydrofolate interconversion
Biological Process	GO:0046653	tetrahydrofolate metabolic process
Molecular Function	GO:0004372	glycine hydroxymethyltransferase activity
Molecular Function	GO:0042802	identical protein binding
Molecular Function	GO:0048027	mRNA 5'-UTR binding
Molecular Function	GO:0000900	mRNA regulatory element binding translation repressor activity
Molecular Function	GO:0042803	protein homodimerization activity
Molecular Function	GO:0030170	pyridoxal phosphate binding
Molecular Function	GO:0070905	serine binding
Molecular Function	GO:0036094	small molecule binding
Molecular Function	GO:0008270	zinc ion binding
Cellular Component	GO:0005737	cytoplasm
Cellular Component	GO:0005829	cytosol
Cellular Component	GO:0070062	extracellular exosome
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus

InterPro / Pfam

InterPro	InterPro name
IPR001085	Serine hydroxymethyltransferase
IPR015421	Pyridoxal phosphate-dependent transferase, major domain
IPR015422	Pyridoxal phosphate-dependent transferase, small domain
IPR015424	Pyridoxal phosphate-dependent transferase
IPR019798	Serine hydroxymethyltransferase, pyridoxal phosphate binding site
IPR039429	Serine hydroxymethyltransferase-like domain

Pfam	Pfam name
PF00464	Serine hydroxymethyltransferase

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-196757	Metabolism of folate and pterines	Leaf	R-HSA-1430728	Metabolism
R-HSA-71262	Carnitine synthesis	Leaf	R-HSA-1430728	Metabolism

Subcellular location

Location	ECO term	Pubmed
Cytoplasm

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
appendix	glandular cells	High	Enhanced
bone marrow	hematopoietic cells	Low	Enhanced
breast	adipocytes	Medium	Enhanced
breast	glandular cells	Medium	Enhanced
breast	myoepithelial cells	Low	Enhanced
bronchus	ciliated cells (cell body)	Low	Enhanced
cerebral cortex	neuropil	Low	Enhanced
cervix	glandular cells	Medium	Enhanced
cervix	squamous epithelial cells	Medium	Enhanced
colon	glandular cells	Medium	Enhanced
duodenum	glandular cells	High	Enhanced
endometrium 1	glandular cells	Medium	Enhanced
endometrium 2	glandular cells	Medium	Enhanced
epididymis	glandular cells	High	Enhanced
esophagus	squamous epithelial cells	Medium	Enhanced
fallopian tube	ciliated cells (cell body)	Low	Enhanced
fallopian tube	ciliated cells (ciliary rootlets)	Medium	Enhanced
gallbladder	glandular cells	Medium	Enhanced
kidney	cells in tubules	High	Enhanced
liver	hepatocytes	High	Enhanced
lung	alveolar cells	Low	Enhanced
lung	macrophages	Medium	Enhanced
oral mucosa	squamous epithelial cells	Low	Enhanced
ovary	follicle cells	Medium	Enhanced
pancreas	exocrine glandular cells	Medium	Enhanced
prostate	glandular cells	Low	Enhanced
rectum	glandular cells	Medium	Enhanced
salivary gland	glandular cells	High	Enhanced
seminal vesicle	glandular cells	Medium	Enhanced
skin 2	epidermal cells	Medium	Enhanced
small intestine	glandular cells	High	Enhanced
stomach 1	glandular cells	Medium	Enhanced
stomach 2	glandular cells	Medium	Enhanced
testis	Leydig cells	Low	Enhanced
testis	elongated or late spermatids	Medium	Enhanced
testis	pachytene spermatocytes	Low	Enhanced
testis	round or early spermatids	Medium	Enhanced
testis	spermatogonia cells	High	Enhanced
thyroid gland	glandular cells	High	Enhanced
tonsil	germinal center cells	Medium	Enhanced
tonsil	squamous epithelial cells	Low	Enhanced
urinary bladder	urothelial cells	Medium	Enhanced
vagina	squamous epithelial cells	Low	Enhanced

Disease

Summary of P34896

Gene: SHMT1
Protein: Serine hydroxymethyltransferase, cytosolic

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of P34896

Gene: SHMT1 Protein: Serine hydroxymethyltransferase, cytosolic

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: SHMT1
Protein: Serine hydroxymethyltransferase, cytosolic