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Q21V29 (GLYA_RHOFD) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 55. 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:Rfer_2658
OrganismRhodoferax ferrireducens (strain DSM 15236 / ATCC BAA-621 / T118) [Complete proteome] [HAMAP]
Taxonomic identifier338969 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › Comamonadaceae › Albidiferax ›

Protein attributes

Sequence length414 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 – 414414Serine hydroxymethyltransferase HAMAP-Rule MF_00051
PRO_1000006305

Regions

Region125 – 1273Substrate binding By similarity

Sites

Binding site351Pyridoxal phosphate By similarity
Binding site551Pyridoxal phosphate By similarity
Binding site571Substrate By similarity
Binding site641Substrate By similarity
Binding site651Pyridoxal phosphate By similarity
Binding site1211Substrate; via carbonyl oxygen By similarity
Binding site1751Pyridoxal phosphate By similarity
Binding site2031Pyridoxal phosphate By similarity
Binding site2281Pyridoxal phosphate By similarity
Binding site2351Pyridoxal phosphate By similarity
Binding site2601Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen By similarity
Binding site3601Pyridoxal phosphate By similarity

Amino acid modifications

Modified residue2291N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence LengthMass (Da)Tools
Q21V29 [UniParc].

Last modified April 18, 2006. Version 1.
Checksum: 337DEC6295847F52

FASTA41444,776
        10         20         30         40         50         60 
MYNRNILIEQ TDPEIFAAIA AENARQEQHI ELIASENYAS PAVMAAQGTQ LTNKYAEGYP 

        70         80         90        100        110        120 
GKRYYGGCEF VDIAEQLAID RVKQIFGADA ANVQPHCGAS ANEAVFLAFL KPGDTIMGMS 

       130        140        150        160        170        180 
LAEGGHLTHG MALNMSGKWF NVVSYGLNDK EEIDYDAMER KAHESKPKLI IAGASAYSLR 

       190        200        210        220        230        240 
IDFARFAKVA KDVGAIFMVD MAHYAGLIAA GIYPNPVPHA DVVTSTTHKS LRGPRGGIIL 

       250        260        270        280        290        300 
MKAQHEKAIN SAIFPGLQGG PLMHVIAAKA VAFKEALQPE FKVYQQQVLT NARVVAETLV 

       310        320        330        340        350        360 
SRGLRIVSGR TESHVMLVDL RSKSITGKEA EAVLGSAHMT INKNAIPNDP EKPMVTSGVR 

       370        380        390        400        410 
IGTPAMTTRG FKDEEARITA NLIADVLDNP RDSANIDAVR AKVNALTKRF PVYG

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References

[1]"Complete sequence of chromosome of Rhodoferax ferrireducens DSM 15236."
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Pitluck S., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Kiss H., Schmutz J., Larimer F., Land M. expand/collapse author list , Kyrpides N., Ivanova N., Richardson P.
Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: DSM 15236 / ATCC BAA-621 / T118.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP000267 Genomic DNA. Translation: ABD70374.1.
RefSeqYP_523905.1. NC_007908.1.

3D structure databases

ProteinModelPortalQ21V29.
SMRQ21V29. Positions 1-414.
ModBaseSearch...

Protein-protein interaction databases

STRING338969.Rfer_2658.

Proteomic databases

PRIDEQ21V29.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABD70374; ABD70374; Rfer_2658.
GeneID3960965.
KEGGrfr:Rfer_2658.
PATRIC23238033. VBIRhoFer131161_3019.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0112.
HOGENOMHOG000239404.
KOK00600.
OMAGFKDEEA.
ProtClustDBPRK00011.

Enzyme and pathway databases

BioCycAFER338969:GHU9-2717-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_RHOFD
AccessionPrimary (citable) accession number: Q21V29
Entry history
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: April 18, 2006
Last modified: May 1, 2013
This is version 55 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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