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Q5LPA8 (GLYA_RUEPO) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 65. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Serine hydroxymethyltransferase
Short name=SHMT
Short name=Serine methylase
EC=2.1.2.1
Gene names
Name:glyA1
Synonyms:glyA-1
Ordered Locus Names:SPO1572
AND
Name:glyA2
Synonyms:glyA-2
Ordered Locus Names:SPO2940
OrganismRuegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (Silicibacter pomeroyi) [Complete proteome] [HAMAP]
Taxonomic identifier246200 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Alphaproteobacteria › Rhodobacterales › Rhodobacteraceae › Ruegeria ›

Protein attributes

Sequence length431 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

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. HAMAP-Rule MF_00051

Catalytic activity

5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine. HAMAP-Rule MF_00051

Cofactor

Pyridoxal phosphate By similarity. HAMAP-Rule MF_00051

Pathway

One-carbon metabolism; tetrahydrofolate interconversion. HAMAP-Rule MF_00051

Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. HAMAP-Rule MF_00051

Subunit structure

Homodimer By similarity. HAMAP-Rule MF_00051

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_00051.

Sequence similarities

Belongs to the SHMT family.

Ontologies

Keywords
   Biological processAmino-acid biosynthesis
One-carbon metabolism
   Cellular componentCytoplasm
   LigandPyridoxal phosphate
   Molecular functionTransferase
   Technical termComplete proteome
Gene Ontology (GO)
   Biological_processglycine biosynthetic process from serine

Inferred from electronic annotation. Source: HAMAP

tetrahydrofolate interconversion

Inferred from electronic annotation. Source: UniProtKB-UniPathway

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionglycine hydroxymethyltransferase activity

Inferred from electronic annotation. Source: HAMAP

pyridoxal phosphate binding

Inferred from electronic annotation. Source: HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 431431Serine hydroxymethyltransferase HAMAP-Rule MF_00051
PRO_0000235024

Regions

Region132 – 1343Substrate binding By similarity

Sites

Binding site421Pyridoxal phosphate By similarity
Binding site621Pyridoxal phosphate By similarity
Binding site641Substrate By similarity
Binding site711Substrate By similarity
Binding site721Pyridoxal phosphate By similarity
Binding site1061Pyridoxal phosphate By similarity
Binding site1281Substrate; via carbonyl oxygen By similarity
Binding site1831Pyridoxal phosphate By similarity
Binding site2111Pyridoxal phosphate By similarity
Binding site2361Pyridoxal phosphate By similarity
Binding site2431Pyridoxal phosphate By similarity
Binding site2691Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen By similarity
Binding site3691Pyridoxal phosphate By similarity

Amino acid modifications

Modified residue2371N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence LengthMass (Da)Tools
Q5LPA8 [UniParc].

Last modified February 1, 2005. Version 1.
Checksum: 74D13D9CB26C1873

FASTA43146,162
        10         20         30         40         50         60 
MNASHQDTGF FTEALSERDP ELFGAITSEL GRQRDEIELI ASENIVSAAV MQAQGSVMTN 

        70         80         90        100        110        120 
KYAEGYPGRR YYGGCQYVDI AENLAIERAK QLFGCGFANV QPNSGSQANQ GVFQALIKPG 

       130        140        150        160        170        180 
DTILGMSLDA GGHLTHGAAP NQSGKWFNAV QYGVRQQDNL LDYDQVEALA KEHRPKLIIA 

       190        200        210        220        230        240 
GGSAIPRQID FARMREIADM VGAYLHVDMA HFAGLVAAGE HPSPFPHAHV ATTTTHKTLR 

       250        260        270        280        290        300 
GPRGGMILTN DEDIAKKVNS AIFPGIQGGP LMHVIAAKAV AFGEALRPEF KTYIQQVIAN 

       310        320        330        340        350        360 
AQALSDQLIK GGLDTVTHGT DTHVVLVDLR PKGVKGNATE KALGRAHITC NKNGVPFDPE 

       370        380        390        400        410        420 
KPTVTSGIRL GSPAGTTRGF AETEFRQIAD WIIEVVDGLA ANGEDANEAV EDKVKAQVAA 

       430 
LCAKFPIYPN L

« Hide

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP000031 Genomic DNA. Translation: AAV96181.1.
CP000031 Genomic DNA. Translation: AAV94859.1.
RefSeqYP_166813.1. NC_003911.11.
YP_168148.1. NC_003911.11.

3D structure databases

ProteinModelPortalQ5LPA8.
SMRQ5LPA8. Positions 15-421.
ModBaseSearch...

Protein-protein interaction databases

STRING246200.SPO2940.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAV94859; AAV94859; SPO1572.
AAV96181; AAV96181; SPO2940.
GeneID3193885.
3194742.
KEGGsil:SPO1572.
sil:SPO2940.
PATRIC23376465. VBIRuePom114501_1597.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0112.
HOGENOMHOG000239404.
KOK00600.
OMAQIDFARM.
ProtClustDBPRK00011.

Enzyme and pathway databases

UniPathwayUPA00193.
UPA00288; UER01023.

Family and domain databases

Gene3D3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPMF_00051. SHMT.
InterProIPR015424. 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]
PANTHERPTHR11680. PTHR11680. 1 hit.
PfamPF00464. SHMT. 1 hit.
[Graphical view]
PIRSFPIRSF000412. SHMT. 1 hit.
SUPFAMSSF53383. PyrdxlP-dep_Trfase_major. 1 hit.
PROSITEPS00096. SHMT. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameGLYA_RUEPO
AccessionPrimary (citable) accession number: Q5LPA8
Entry history
Integrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: February 1, 2005
Last modified: May 1, 2013
This is version 65 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

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