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Protein

Serine hydroxymethyltransferase

Gene

glyA

Organism
Anabaena variabilis (strain ATCC 29413 / PCC 7937)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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.UniRule annotation

Catalytic activityi

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

Cofactori

pyridoxal 5'-phosphateUniRule annotation

Pathwayi: tetrahydrofolate interconversion

This protein is involved in the pathway tetrahydrofolate interconversion, which is part of One-carbon metabolism.UniRule annotation
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.UniRule annotation
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 sitei36Pyridoxal phosphateUniRule annotation1
Binding sitei56Pyridoxal phosphateUniRule annotation1
Binding sitei58SubstrateUniRule annotation1
Binding sitei65SubstrateUniRule annotation1
Binding sitei66Pyridoxal phosphateUniRule annotation1
Binding sitei122Substrate; via carbonyl oxygenUniRule annotation1
Binding sitei177Pyridoxal phosphateUniRule annotation1
Binding sitei205Pyridoxal phosphateUniRule annotation1
Binding sitei230Pyridoxal phosphateUniRule annotation1
Binding sitei237Pyridoxal phosphateUniRule annotation1
Binding sitei263Pyridoxal phosphate; via amide nitrogen and carbonyl oxygenUniRule annotation1
Binding sitei363Pyridoxal phosphateUniRule annotation1

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

BioCyciAVAR240292:G7WH-10281-MONOMER.
UniPathwayiUPA00193.
UPA00288; UER01023.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine hydroxymethyltransferaseUniRule annotation (EC:2.1.2.1UniRule annotation)
Short name:
SHMTUniRule annotation
Short name:
Serine methylaseUniRule annotation
Gene namesi
Name:glyAUniRule annotation
Ordered Locus Names:Ava_2076
OrganismiAnabaena variabilis (strain ATCC 29413 / PCC 7937)
Taxonomic identifieri240292 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaNostocalesNostocaceaeAnabaena
Proteomesi
  • UP000002533 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002349441 – 427Serine hydroxymethyltransferaseAdd BLAST427

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei231N6-(pyridoxal phosphate)lysineUniRule annotation1

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi240292.Ava_2076.

Structurei

3D structure databases

ProteinModelPortaliQ3MBD8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni126 – 128Substrate bindingUniRule annotation3
Regioni355 – 357Substrate bindingUniRule annotation3

Sequence similaritiesi

Belongs to the SHMT family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C65. Bacteria.
COG0112. LUCA.
HOGENOMiHOG000239404.
KOiK00600.
OMAiAAWANVQ.
OrthoDBiPOG091H02WA.

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.

Q3MBD8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTRTNSDFLT NSDPAIAGLI NQELQRQRDH LELIASENFT SAAVLAAQGS
60 70 80 90 100
VLTNKYAEGL PGKRYYGGCE FIDKIEQIAI DRAKQLFGAA HANVQPHSGA
110 120 130 140 150
QANFAVFLTL LAPGDKIMGM DLSHGGHLTH GSPVNVSGKW FQVCHYGVSQ
160 170 180 190 200
QTEQLDYDQI RELALRERPK LLICGYSAYP RIIDFEKFRS IADEVGAYLL
210 220 230 240 250
ADIAHIAGLV ASGLHPDPIP YCHVVTTTTH KTLRGPRGGL ILTGDAELGK
260 270 280 290 300
KLDKSVFPGS QGGPLEHVIA GKAVAFGEAL KPEFQGYSAQ VIENARALAN
310 320 330 340 350
QLQNRGLKLV SDGTDNHLML VDLRSVNMTG KRADQLVSEV NITANKNTVP
360 370 380 390 400
FDPQSPFVTS GLRLGSPAMT TRGMGEAEFT EIGNIIADRL LNPDSDTVAQ
410 420
DCKRRVAALC DRFPLYPHLE IPVPVLA
Length:427
Mass (Da):46,272
Last modified:October 25, 2005 - v1
Checksum:i11EF119715721354
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000117 Genomic DNA. Translation: ABA21698.1.

Genome annotation databases

EnsemblBacteriaiABA21698; ABA21698; Ava_2076.
KEGGiava:Ava_2076.
PATRICi35424891. VBIAnaVar43351_3000.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000117 Genomic DNA. Translation: ABA21698.1.

3D structure databases

ProteinModelPortaliQ3MBD8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi240292.Ava_2076.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABA21698; ABA21698; Ava_2076.
KEGGiava:Ava_2076.
PATRICi35424891. VBIAnaVar43351_3000.

Phylogenomic databases

eggNOGiENOG4105C65. Bacteria.
COG0112. LUCA.
HOGENOMiHOG000239404.
KOiK00600.
OMAiAAWANVQ.
OrthoDBiPOG091H02WA.

Enzyme and pathway databases

UniPathwayiUPA00193.
UPA00288; UER01023.
BioCyciAVAR240292:G7WH-10281-MONOMER.

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_ANAVT
AccessioniPrimary (citable) accession number: Q3MBD8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: October 25, 2005
Last modified: November 2, 2016
This is version 76 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

Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.