P37292 (GLYM_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Serine hydroxymethyltransferase, mitochondrial
Short name=SHMT
EC=2.1.2.1

Alternative name(s):
Glycine hydroxymethyltransferase
Serine methylase

Gene names

Name:	SHM1
Synonyms:	SHMT1
Ordered Locus Names:	YBR263W
ORF Names:	YBR1732

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	490 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	Interconversion of serine and glycine.
Catalytic activity	5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.
Cofactor	Pyridoxal phosphate.
Pathway	One-carbon metabolism; tetrahydrofolate interconversion.
Subunit structure	Homotetramer By similarity. Interacts with NAP1. Ref.6
Subcellular location	Mitochondrion.
Miscellaneous	In eukaryotes there are two forms of the enzymes: a cytosolic one and a mitochondrial one. Present with 17700 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the SHMT family.
Sequence caution	The sequence CAA49927.1 differs from that shown. Reason: Erroneous initiation. The sequence CAA85226.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	One-carbon metabolism
Cellular component	Mitochondrion
Domain	Transit peptide
Ligand	Pyridoxal phosphate
Molecular function	Transferase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	L-serine metabolic process Inferred from electronic annotation. Source: InterPro glycine metabolic process Inferred from electronic annotation. Source: InterPro one-carbon metabolic process Inferred from mutant phenotype PubMed 1100397. Source: SGD serine family amino acid biosynthetic process Inferred from genetic interaction PubMed 9398220. Source: SGD tetrahydrofolate interconversion Inferred from electronic annotation. Source: UniProtKB-UniPathway
Cellular_component	mitochondrion Inferred from direct assay PubMed 14576278PubMed 16823961. Source: SGD
Molecular_function	glycine hydroxymethyltransferase activity Inferred from mutant phenotype PubMed 1100397. Source: SGD pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 20	20	Mitochondrion Potential
	Chain	21 – 490	470	Serine hydroxymethyltransferase, mitochondrial		PRO_0000032568
Amino acid modifications
	Modified residue	265	1	N6-(pyridoxal phosphate)lysine By similarity
Experimental info
	Sequence conflict	72	1	L → S in AAA21024. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P37292 [UniParc]. Last modified December 6, 2005. Version 2. Checksum: 8DECF1ECD6349450	FASTA	490	53,686
	10 20 30 40 50 60 MFPRASALAK CMATVHRRGL LTSGAQSLVS KPVSEGDPEM FDILQQERHR QKHSITLIPS 70 80 90 100 110 120 ENFTSKAVMD LLGSELQNKY SEGYPGERYY GGNEIIDKSE SLCQARALEL YGLDPAKWGV 130 140 150 160 170 180 NVQPLSGAPA NLYVYSAIMN VGERLMGLDL PDGGHLSHGY QLKSGTPISF ISKYFQSMPY 190 200 210 220 230 240 HVDHTTGLID YDNLQVLAKA FRPKVIVAGT SAYSRLIDYA RFKEISQGCG AYLMSDMAHI 250 260 270 280 290 300 SGLVAANVVP SPFEHSDIVT TTTHKSLRGP RGAMIFFRKG IKSVTKKGKE IPYELEKKIN 310 320 330 340 350 360 FSVFPGHQGG PHNHTIGAMA VALKQAMSPE FKEYQQKIVD NSKWFAQELT KMGYKLVSGG 370 380 390 400 410 420 TDNHLIVIDL SGTQVDGARV ETILSALNIA ANKNTIPGDK SALFPSGLRI GTPAMTTRGF 430 440 450 460 470 480 GREEFSQVAK YIDSAVKLAE NLKTLEPTTK LDARSRLNEF KKLCNESSEV AALSGEISKW 490 VGQYPVPGDI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and molecular characterization of three genes, including two genes encoding serine hydroxymethyltransferases, whose inactivation is required to render yeast auxotrophic for glycine." McNeil J.B., McIntosh E.M., Taylor B.V., Zhang F.-R., Tang S., Bognar A.L. J. Biol. Chem. 269:9155-9165(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 208353 / W303-1A.
[2]	"The complete sequence of a 19,482 bp segment located on the right arm of chromosome II from Saccharomyces cerevisiae." Doignon F., Biteau N., Crouzet M., Aigle M. Yeast 9:189-199(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"Complete DNA sequence of yeast chromosome II." Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K. EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[6]	"Phosphorylation by casein kinase 2 regulates Nap1 localization and function." Calvert M.E.K., Keck K.M., Ptak C., Shabanowitz J., Hunt D.F., Pemberton L.F. Mol. Cell. Biol. 28:1313-1325(2008) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH NAP1, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	L22528 Genomic DNA. Translation: AAA21024.1. X70529 Genomic DNA. Translation: CAA49927.1. Different initiation. Z36131 Genomic DNA. Translation: CAA85226.1. Different initiation. BK006936 Genomic DNA. Translation: DAA07380.1.
PIR	S29348.
RefSeq	NP_009822.4. NM_001178611.3.
3D structure databases
ProteinModelPortal	P37292.
SMR	P37292. Positions 23-488.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-4952N.
IntAct	P37292. 3 interactions.
MINT	MINT-548725.
STRING	4932.YBR263W.
Proteomic databases
PaxDb	P37292.
PeptideAtlas	P37292.
PRIDE	P37292.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YBR263W; YBR263W; YBR263W.
GeneID	852565.
KEGG	sce:YBR263W.
Organism-specific databases
CYGD	YBR263w.
SGD	S000000467. SHM1.
Phylogenomic databases
eggNOG	COG0112.
GeneTree	ENSGT00390000002762.
HOGENOM	HOG000239405.
KO	K00600.
OMA	GFNENDV.
OrthoDB	EOG4V1B88.
Enzyme and pathway databases
BioCyc	MetaCyc:YBR263W-MONOMER. YEAST:YBR263W-MONOMER.
UniPathway	UPA00193.
Gene expression databases
Genevestigator	P37292.
GermOnline	YBR263W. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	3.40.640.10. 1 hit. 3.90.1150.10. 1 hit.
InterPro	IPR015424. PyrdxlP-dep_Trfase. IPR015421. PyrdxlP-dep_Trfase_major_sub1. IPR015422. PyrdxlP-dep_Trfase_major_sub2. IPR001085. Ser_HO-MeTrfase. IPR019798. Ser_HO-MeTrfase_PLP_BS. [Graphical view]
PANTHER	PTHR11680. PTHR11680. 1 hit.
Pfam	PF00464. SHMT. 1 hit. [Graphical view]
PIRSF	PIRSF000412. SHMT. 1 hit.
SUPFAM	SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.
PROSITE	PS00096. SHMT. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	971682.

Entry information

Entry name

GLYM_YEAST

Accession

Primary (citable) accession number: P37292
Secondary accession number(s): D6VQR0

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	December 6, 2005
Last modified:	May 29, 2013
This is version 120 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program