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B1IJJ8 (GLYA_CLOBK) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 42. 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:CLD_1970
OrganismClostridium botulinum (strain Okra / Type B1) [Complete proteome] [HAMAP]
Taxonomic identifier498213 [NCBI]
Taxonomic lineageBacteria › Firmicutes › Clostridia › Clostridiales › Clostridiaceae › Clostridium ›

Protein attributes

Sequence length413 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.

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.

Subcellular location

Cytoplasm By similarity.

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 – 413413Serine hydroxymethyltransferase HAMAP-Rule MF_00051
PRO_1000091531

Regions

Region123 – 1253Substrate binding By similarity
Region351 – 3533Substrate 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 site2591Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen By similarity
Binding site3591Pyridoxal phosphate By similarity

Amino acid modifications

Modified residue2281N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence LengthMass (Da)Tools
B1IJJ8 [UniParc].

Last modified April 29, 2008. Version 1.
Checksum: 14B4C4EB8DE7D541

FASTA41346,327
        10         20         30         40         50         60 
MDFTNLKNTD PELLDMIKKE EERQEYNIEL IASENFTSLS VMEAMGSLLT NKYAEGYPHK 

        70         80         90        100        110        120 
RYYGGCEFVD EVEDLARERL KKLFVAEHAN VQPHSGSQAN MAVYMSVLQT GDTILGMDLS 

       130        140        150        160        170        180 
HGGHLTHGSP VNFSGKLYNF ISYGVDKETE TIDYDQLKKI ALENRPKMIV SGASAYPRII 

       190        200        210        220        230        240 
DFEKIREICD EIDAYMMVDM AHIAGLVATG IHPSPVPYAD FVTTTTHKTL RGPRGGAILC 

       250        260        270        280        290        300 
KEKYAKAVDK AIFPGIQGGP LMHTIAAKAV CFGEALREDY KEYMQQVVKN TKVLGEELKN 

       310        320        330        340        350        360 
YGFRLISGGT DNHLLLIDLT NKNITGKDAE KLLDSVGITV NKNTIPFETL SPFITSGIRI 

       370        380        390        400        410 
GTPAVTTRGF KEEEMKKIAY FMNYSIEHRE ENLSQIKEQI KEICKKYPLH QNA

« Hide

References

[1]"Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids."
Smith T.J., Hill K.K., Foley B.T., Detter J.C., Munk A.C., Bruce D.C., Doggett N.A., Smith L.A., Marks J.D., Xie G., Brettin T.S.
PLoS ONE 2:E1271-E1271(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Okra / Type B1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP000939 Genomic DNA. Translation: ACA44798.1.
RefSeqYP_001782210.1. NC_010516.1.

3D structure databases

ProteinModelPortalB1IJJ8.
SMRB1IJJ8. Positions 6-400.
ModBaseSearch...

Protein-protein interaction databases

STRING498213.CLD_1970.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACA44798; ACA44798; CLD_1970.
GeneID6149803.
KEGGcbb:CLD_1970.
PATRIC19405570. VBICloBot127283_2689.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0112.
HOGENOMHOG000239404.
KOK00600.
OMAHMVLVDV.
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_CLOBK
AccessionPrimary (citable) accession number: B1IJJ8
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 29, 2008
Last modified: May 1, 2013
This is version 42 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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