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Protein

Serine hydroxymethyltransferase

Gene

glyA

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism (By similarity).By similarity

Catalytic activityi

5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.

Cofactori

Pathwayi: tetrahydrofolate interconversion

This protein is involved in the pathway tetrahydrofolate interconversion, which is part of One-carbon metabolism.
View all proteins of this organism that are known to be involved in the pathway tetrahydrofolate interconversion and in One-carbon metabolism.

Pathwayi: glycine biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes glycine from L-serine.
Proteins known to be involved in this subpathway in this organism are:
  1. Serine hydroxymethyltransferase (glyA)
This subpathway is part of the pathway glycine biosynthesis, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes glycine from L-serine, the pathway glycine biosynthesis and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei35Pyridoxal phosphateBy similarity1
Binding sitei55Pyridoxal phosphateBy similarity1
Binding sitei57SubstrateBy similarity1
Binding sitei64SubstrateBy similarity1
Binding sitei65Pyridoxal phosphateBy similarity1
Binding sitei99Pyridoxal phosphateBy similarity1
Binding sitei121Substrate; via carbonyl oxygenBy similarity1
Binding sitei175Pyridoxal phosphateBy similarity1
Binding sitei203Pyridoxal phosphateBy similarity1
Binding sitei228Pyridoxal phosphateBy similarity1
Binding sitei235Pyridoxal phosphateBy similarity1
Binding sitei263Pyridoxal phosphate; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei363Pyridoxal phosphateBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Amino-acid biosynthesis, One-carbon metabolism

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

UniPathwayiUPA00193.
UPA00288; UER01023.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine hydroxymethyltransferase (EC:2.1.2.1)
Short name:
SHMT
Short name:
Serine methylase
Gene namesi
Name:glyA
Ordered Locus Names:STM2555
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001136581 – 417Serine hydroxymethyltransferaseAdd BLAST417

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei229N6-(pyridoxal phosphate)lysine1

Proteomic databases

PaxDbiP0A2E1.
PRIDEiP0A2E1.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi99287.STM2555.

Structurei

Secondary structure

1417
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni3 – 5Combined sources3
Helixi8 – 11Combined sources4
Helixi13 – 28Combined sources16
Beta strandi29 – 31Combined sources3
Helixi41 – 47Combined sources7
Helixi50 – 53Combined sources4
Helixi72 – 86Combined sources15
Beta strandi89 – 92Combined sources4
Helixi98 – 109Combined sources12
Beta strandi115 – 121Combined sources7
Helixi136 – 139Combined sources4
Beta strandi140 – 147Combined sources8
Helixi155 – 165Combined sources11
Beta strandi168 – 172Combined sources5
Helixi183 – 192Combined sources10
Beta strandi196 – 200Combined sources5
Turni202 – 204Combined sources3
Helixi205 – 209Combined sources5
Turni217 – 219Combined sources3
Beta strandi220 – 228Combined sources9
Helixi229 – 231Combined sources3
Beta strandi237 – 243Combined sources7
Helixi246 – 255Combined sources10
Helixi266 – 278Combined sources13
Helixi282 – 304Combined sources23
Helixi310 – 312Combined sources3
Beta strandi315 – 322Combined sources8
Helixi324 – 326Combined sources3
Helixi330 – 339Combined sources10
Beta strandi345 – 347Combined sources3
Turni356 – 358Combined sources3
Beta strandi360 – 365Combined sources6
Helixi367 – 371Combined sources5
Helixi376 – 391Combined sources16
Turni392 – 394Combined sources3
Helixi396 – 412Combined sources17

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3GBXX-ray1.80A/B1-417[»]
ProteinModelPortaliP0A2E1.
SMRiP0A2E1.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A2E1.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni125 – 127Substrate bindingBy similarity3
Regioni355 – 357Substrate bindingBy similarity3

Sequence similaritiesi

Belongs to the SHMT family.Curated

Phylogenomic databases

eggNOGiENOG4105C65. Bacteria.
COG0112. LUCA.
HOGENOMiHOG000239403.
KOiK00600.
OMAiAAWANVQ.
PhylomeDBiP0A2E1.

Family and domain databases

CDDicd00378. SHMT. 1 hit.
Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPiMF_00051. SHMT. 1 hit.
InterProiIPR015424. 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]
PANTHERiPTHR11680. PTHR11680. 1 hit.
PfamiPF00464. SHMT. 1 hit.
[Graphical view]
PIRSFiPIRSF000412. SHMT. 1 hit.
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00096. SHMT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A2E1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLKREMNIAD YDAELWQAME QEKVRQEEHI ELIASENYTS PRVMQAQGSQ
60 70 80 90 100
LTNKYAEGYP GKRYYGGCEY VDVVEQLAID RAKELFGADY ANVQPHSGSQ
110 120 130 140 150
ANFAVYTALL QPGDTVLGMN LAQGGHLTHG SPVNFSGKLY NIVPYGIDES
160 170 180 190 200
GKIDYDEMAK LAKEHKPKMI IGGFSAYSGV VDWAKMREIA DSIGAYLFVD
210 220 230 240 250
MAHVAGLIAA GVYPNPVPHA HVVTTTTHKT LAGPRGGLIL AKGGDEELYK
260 270 280 290 300
KLNSAVFPSA QGGPLMHVIA GKAVALKEAM EPEFKVYQQQ VAKNAKAMVE
310 320 330 340 350
VFLNRGYKVV SGGTENHLFL LDLVDKNLTG KEADAALGRA NITVNKNSVP
360 370 380 390 400
NDPKSPFVTS GIRIGSPAVT RRGFKEAEVK ELAGWMCDVL DNINDEATIE
410
RVKAKVLDIC ARFPVYA
Length:417
Mass (Da):45,455
Last modified:March 15, 2005 - v1
Checksum:i3AA2E7EAF302042C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti161L → S in CAA33808 (PubMed:2134182).Curated1
Sequence conflicti193I → Y in AAA27135 (PubMed:6325301).Curated1
Sequence conflicti275A → G in CAA33808 (PubMed:2134182).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15816 Genomic DNA. Translation: CAA33808.1.
AE006468 Genomic DNA. Translation: AAL21449.1.
K01616 Genomic DNA. Translation: AAA27135.1.
PIRiB48427.
RefSeqiNP_461490.1. NC_003197.1.
WP_000919178.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL21449; AAL21449; STM2555.
GeneIDi1254077.
KEGGistm:STM2555.
PATRICi32383745. VBISalEnt20916_2695.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15816 Genomic DNA. Translation: CAA33808.1.
AE006468 Genomic DNA. Translation: AAL21449.1.
K01616 Genomic DNA. Translation: AAA27135.1.
PIRiB48427.
RefSeqiNP_461490.1. NC_003197.1.
WP_000919178.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3GBXX-ray1.80A/B1-417[»]
ProteinModelPortaliP0A2E1.
SMRiP0A2E1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM2555.

Proteomic databases

PaxDbiP0A2E1.
PRIDEiP0A2E1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL21449; AAL21449; STM2555.
GeneIDi1254077.
KEGGistm:STM2555.
PATRICi32383745. VBISalEnt20916_2695.

Phylogenomic databases

eggNOGiENOG4105C65. Bacteria.
COG0112. LUCA.
HOGENOMiHOG000239403.
KOiK00600.
OMAiAAWANVQ.
PhylomeDBiP0A2E1.

Enzyme and pathway databases

UniPathwayiUPA00193.
UPA00288; UER01023.

Miscellaneous databases

EvolutionaryTraceiP0A2E1.

Family and domain databases

CDDicd00378. SHMT. 1 hit.
Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPiMF_00051. SHMT. 1 hit.
InterProiIPR015424. 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]
PANTHERiPTHR11680. PTHR11680. 1 hit.
PfamiPF00464. SHMT. 1 hit.
[Graphical view]
PIRSFiPIRSF000412. SHMT. 1 hit.
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00096. SHMT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiGLYA_SALTY
AccessioniPrimary (citable) accession number: P0A2E1
Secondary accession number(s): P06192
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: March 15, 2005
Last modified: November 2, 2016
This is version 84 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.