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C0QQE4 (GLYA_PERMH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 33. 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:PERMA_1104
OrganismPersephonella marina (strain DSM 14350 / EX-H1) [Complete proteome] [HAMAP]
Taxonomic identifier123214 [NCBI]
Taxonomic lineageBacteria › Aquificae › Aquificales › Hydrogenothermaceae › Persephonella ›

Protein attributes

Sequence length420 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 – 420420Serine hydroxymethyltransferase HAMAP-Rule MF_00051
PRO_1000117645

Regions

Region122 – 1243Substrate binding By similarity

Sites

Binding site321Pyridoxal phosphate By similarity
Binding site521Pyridoxal phosphate By similarity
Binding site541Substrate By similarity
Binding site611Substrate By similarity
Binding site621Pyridoxal phosphate By similarity
Binding site961Pyridoxal phosphate By similarity
Binding site1181Substrate; via carbonyl oxygen By similarity
Binding site1731Pyridoxal phosphate By similarity
Binding site2011Pyridoxal phosphate By similarity
Binding site2261Pyridoxal phosphate By similarity
Binding site2331Pyridoxal phosphate By similarity
Binding site2581Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen By similarity
Binding site3581Pyridoxal phosphate By similarity

Amino acid modifications

Modified residue2271N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence LengthMass (Da)Tools
C0QQE4 [UniParc].

Last modified May 5, 2009. Version 1.
Checksum: B26BC543BABF8C0A

FASTA42046,650
        10         20         30         40         50         60 
MLKHLKQVDQ EVFEAVSKEF KRQQEHLEMI ASENYTSYAV MEAQGSVLTN KYAEGLPHKR 

        70         80         90        100        110        120 
YYGGCEYVDI VEDLAIERLK KIYGAEHANV QPHSGSQANQ AVYFSQLQAG DTIMGMSLAH 

       130        140        150        160        170        180 
GGHLTHGAKV NLSGIVFNAV QYGVNPETEL IDYDQVYKLA KEHKPKMIVA GASAYSRIID 

       190        200        210        220        230        240 
WAKFREIADE VGALLMVDMA HYAGLIAGGA YPSPVPYADF VTSTTHKTLR GPRGGFILSK 

       250        260        270        280        290        300 
AQYGKDIDKW VFPRLQGGPL MHVIAAKAVA FKEAMTEEFR EYAHQTVKNA KVLAEELKAE 

       310        320        330        340        350        360 
GLRIVSGGTD SHIVLVDLRP LNVKGNQAEE ALGRANITVN KNAIPFDPEK PMVTSGIRLG 

       370        380        390        400        410        420 
TAALTTRGMK ENDMRRIAKN IVKVLKNLDN EKIIQEVKDD VLSLCSSYPL YPEWTEYYLD

« Hide

References

[1]"Complete and draft genome sequences of six members of the Aquificales."
Reysenbach A.-L., Hamamura N., Podar M., Griffiths E., Ferreira S., Hochstein R., Heidelberg J., Johnson J., Mead D., Pohorille A., Sarmiento M., Schweighofer K., Seshadri R., Voytek M.A.
J. Bacteriol. 191:1992-1993(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: DSM 14350 / EX-H1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP001230 Genomic DNA. Translation: ACO03855.1.
RefSeqYP_002730890.1. NC_012440.1.

3D structure databases

ProteinModelPortalC0QQE4.
ModBaseSearch...

Protein-protein interaction databases

STRING123214.PERMA_1104.

Proteomic databases

PRIDEC0QQE4.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACO03855; ACO03855; PERMA_1104.
GeneID7674236.
KEGGpmx:PERMA_1104.
PATRIC22915671. VBIPerMar119911_1142.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0112.
HOGENOMHOG000239403.
KOK00600.
OMAGKIDYED.
ProtClustDBPRK00011.

Enzyme and pathway databases

BioCycPMAR123214:GIZP-1103-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_PERMH
AccessionPrimary (citable) accession number: C0QQE4
Entry history
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: May 5, 2009
Last modified: May 1, 2013
This is version 33 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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