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Protein

Serine hydroxymethyltransferase

Gene

glyA

Organism
Rhizobium etli (strain CFN 42 / ATCC 51251)
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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei41 – 411Pyridoxal phosphateUniRule annotation
Binding sitei61 – 611Pyridoxal phosphateUniRule annotation
Binding sitei63 – 631SubstrateUniRule annotation
Binding sitei70 – 701SubstrateUniRule annotation
Binding sitei71 – 711Pyridoxal phosphateUniRule annotation
Binding sitei105 – 1051Pyridoxal phosphateUniRule annotation
Binding sitei127 – 1271Substrate; via carbonyl oxygenUniRule annotation
Binding sitei182 – 1821Pyridoxal phosphateUniRule annotation
Binding sitei210 – 2101Pyridoxal phosphateUniRule annotation
Binding sitei235 – 2351Pyridoxal phosphateUniRule annotation
Binding sitei242 – 2421Pyridoxal phosphateUniRule annotation
Binding sitei268 – 2681Pyridoxal phosphate; via amide nitrogen and carbonyl oxygenUniRule annotation
Binding sitei368 – 3681Pyridoxal phosphateUniRule annotation

GO - Molecular functioni

  1. glycine hydroxymethyltransferase activity Source: UniProtKB-HAMAP
  2. pyridoxal phosphate binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. glycine biosynthetic process from serine Source: UniProtKB-HAMAP
  2. tetrahydrofolate interconversion Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Amino-acid biosynthesis, One-carbon metabolism

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciRETL347834:GJJ0-1517-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:RHE_CH01508
OrganismiRhizobium etli (strain CFN 42 / ATCC 51251)
Taxonomic identifieri347834 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupRhizobium
ProteomesiUP000001936: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 432432Serine hydroxymethyltransferasePRO_1000006303Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei236 – 2361N6-(pyridoxal phosphate)lysineUniRule annotation

Proteomic databases

PRIDEiQ2KA25.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi347834.RHE_CH01508.

Structurei

3D structure databases

ProteinModelPortaliQ2KA25.
SMRiQ2KA25. Positions 12-423.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni131 – 1333Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the SHMT family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0112.
HOGENOMiHOG000239404.
KOiK00600.
OMAiAAWANVQ.
OrthoDBiEOG6Z0QB2.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPiMF_00051. SHMT.
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.

Q2KA25-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTNASTESFF NRSLADVDPE IFGAIGKELG RQRHEIELIA SENIVSRAVL
60 70 80 90 100
EAQGSIMTNK YAEGYPGKRY YGGCQFVDIA EELAIERAKK LFGVNFANVQ
110 120 130 140 150
PNSGSQMNQA VFLALLQPGD TFMGLDLNSG GHLTHGSPVN MSGKWFNVVS
160 170 180 190 200
YGVREGDNLL DMDEVARKAE EHKPKVIIAG GTAYSRIWDW KRFREIADSV
210 220 230 240 250
GAYLMVDMAH IAGLVAGGQH PSPFPHCHVA TTTTHKSLRG PRGGVILTNE
260 270 280 290 300
EDLAKKFNSA VFPGLQGGPL MHIIAAKAVA FGEALQPEFK EYAAQIVKNA
310 320 330 340 350
RALAETLIAG GLDVVSGGTD NHLMLVDLRK KNATGKRAEA ALGRAYITCN
360 370 380 390 400
KNGIPFDPEK PFVTSGVRLG APAGTTRGFK EAEFREIGNL IVEVLDGLKV
410 420 430
ANSDDGNAAV EAAVRGKVVN LTDRFPMYDY MG
Length:432
Mass (Da):46,598
Last modified:March 7, 2006 - v1
Checksum:iF8CF2FDAD295117D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000133 Genomic DNA. Translation: ABC90311.1.
RefSeqiWP_011424840.1. NC_007761.1.
YP_469038.1. NC_007761.1.

Genome annotation databases

EnsemblBacteriaiABC90311; ABC90311; RHE_CH01508.
GeneIDi3890943.
KEGGiret:RHE_CH01508.
PATRICi23084429. VBIRhiEtl108884_1886.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000133 Genomic DNA. Translation: ABC90311.1.
RefSeqiWP_011424840.1. NC_007761.1.
YP_469038.1. NC_007761.1.

3D structure databases

ProteinModelPortaliQ2KA25.
SMRiQ2KA25. Positions 12-423.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi347834.RHE_CH01508.

Proteomic databases

PRIDEiQ2KA25.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABC90311; ABC90311; RHE_CH01508.
GeneIDi3890943.
KEGGiret:RHE_CH01508.
PATRICi23084429. VBIRhiEtl108884_1886.

Phylogenomic databases

eggNOGiCOG0112.
HOGENOMiHOG000239404.
KOiK00600.
OMAiAAWANVQ.
OrthoDBiEOG6Z0QB2.

Enzyme and pathway databases

UniPathwayiUPA00193.
UPA00288; UER01023.
BioCyciRETL347834:GJJ0-1517-MONOMER.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPiMF_00051. SHMT.
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...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CFN 42 / ATCC 51251.

Entry informationi

Entry nameiGLYA_RHIEC
AccessioniPrimary (citable) accession number: Q2KA25
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: March 7, 2006
Last modified: February 4, 2015
This is version 63 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, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.