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B4SE31 (GLYA_PELPB) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 38. 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:glyA
Ordered Locus Names:Ppha_0727
OrganismPelodictyon phaeoclathratiforme (strain DSM 5477 / BU-1) [Complete proteome] [HAMAP]
Taxonomic identifier324925 [NCBI]
Taxonomic lineageBacteria › Chlorobi › Chlorobia › Chlorobiales › Chlorobiaceae › Chlorobium/Pelodictyon group › Pelodictyon ›

Protein attributes

Sequence length438 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 – 438438Serine hydroxymethyltransferase HAMAP-Rule MF_00051
PRO_1000091565

Regions

Region123 – 1253Substrate binding By similarity
Region370 – 3723Substrate binding By similarity

Sites

Binding site331Pyridoxal phosphate By similarity
Binding site531Pyridoxal phosphate By similarity
Binding site551Substrate By similarity
Binding site621Substrate By similarity
Binding site631Pyridoxal phosphate By similarity
Binding site971Pyridoxal phosphate By similarity
Binding site1191Substrate; via carbonyl oxygen By similarity
Binding site1741Pyridoxal phosphate By similarity
Binding site2021Pyridoxal phosphate By similarity
Binding site2271Pyridoxal phosphate By similarity
Binding site2341Pyridoxal phosphate By similarity
Binding site2781Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen By similarity
Binding site3781Pyridoxal phosphate By similarity

Amino acid modifications

Modified residue2281N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence LengthMass (Da)Tools
B4SE31 [UniParc].

Last modified September 23, 2008. Version 1.
Checksum: 98C95515A945B09E

FASTA43847,292
        10         20         30         40         50         60 
MDTDILQKQD SELFEAIAKE TGRQTETLEL IASENFTSRA VMQACGSVMT NKYAEGYPGK 

        70         80         90        100        110        120 
RYYGGCEFVD IAENLARDRA KKLFGCDYVN VQPHSGSSAN MAVLFSVLKP GDRIMGLDLS 

       130        140        150        160        170        180 
HGGHLTHGSS VNFSGQMYEA HSYGVDRETG CIDMNKVEEL ALQVRPKLII CGASAYSQGF 

       190        200        210        220        230        240 
DVKAFRVIAD KVGAFLMADI AHPAGLIAAG LLGNPLPHCH FVTTTTHKTL RGPRGGMIMM 

       250        260        270        280        290        300 
GSDFENPMGI TIKTKTGSRL KMMSEVMDAE VMPGIQGGPL MHIIAGKAVA FGEALQPAFR 

       310        320        330        340        350        360 
DYAAQVIKNA AAMAEKFTEL GYKIVSGGTK NHLMLLDLRS KNVTGKVAEN LLHSAGITVN 

       370        380        390        400        410        420 
KNMVPFDDKS PFVTSGIRVG TPAMTTRGMN EADSVLIAEL IDRVITSAEK PDVADLCRSV 

       430 
REEIKALCLR NPIDGYTV

« Hide

References

[1]"Complete sequence of Pelodictyon phaeoclathratiforme BU-1."
US DOE Joint Genome Institute
Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Liu Z., Li T., Zhao F. expand/collapse author list , Overmann J., Bryant D.A., Richardson P.
Submitted (JUN-2008) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: DSM 5477 / BU-1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP001110 Genomic DNA. Translation: ACF43022.1.
RefSeqYP_002017639.1. NC_011060.1.

3D structure databases

ProteinModelPortalB4SE31.
SMRB4SE31. Positions 8-433.
ModBaseSearch...

Protein-protein interaction databases

STRING324925.Ppha_0727.

Proteomic databases

PRIDEB4SE31.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACF43022; ACF43022; Ppha_0727.
GeneID6461436.
KEGGpph:Ppha_0727.
PATRIC22901890. VBIPelPha134556_0737.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0112.
HOGENOMHOG000239404.
KOK00600.
OMAHMVLVDV.
ProtClustDBPRK00011.

Enzyme and pathway databases

BioCycPPHA324925:GHBF-741-MONOMER.
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_PELPB
AccessionPrimary (citable) accession number: B4SE31
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: September 23, 2008
Last modified: May 1, 2013
This is version 38 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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