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Q3J9K8 (GLYA_NITOC) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 59. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

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:Noc_2027
OrganismNitrosococcus oceani (strain ATCC 19707 / NCIMB 11848) [Complete proteome] [HAMAP]
Taxonomic identifier323261 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Chromatiales › Chromatiaceae › Nitrosococcus ›

Protein attributes

Sequence length417 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 – 417417Serine hydroxymethyltransferase HAMAP-Rule MF_00051
PRO_0000234992

Regions

Region125 – 1273Substrate binding By similarity
Region355 – 3573Substrate 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 site991Pyridoxal phosphate By similarity
Binding site1211Substrate; via carbonyl oxygen By similarity
Binding site1761Pyridoxal phosphate By similarity
Binding site2041Pyridoxal phosphate By similarity
Binding site2291Pyridoxal phosphate By similarity
Binding site2361Pyridoxal phosphate By similarity
Binding site2631Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen By similarity
Binding site3631Pyridoxal phosphate By similarity

Amino acid modifications

Modified residue2301N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence LengthMass (Da)Tools
Q3J9K8 [UniParc].

Last modified November 8, 2005. Version 1.
Checksum: FF1EBE0718CF3872

FASTA41744,998
        10         20         30         40         50         60 
MYSKEMRIAS YDEELETALT NEARRQEEHI ELIASENYVS PRVLEAQGSV LTNKYAEGYP 

        70         80         90        100        110        120 
GKRYYGGCEY VDVAERLAIE RAKILFEADY ANVQPHSGSQ ANAAACLALL APGDTLMGLS 

       130        140        150        160        170        180 
LAHGGHLTHG AKVNFSGQIF NAVQFGVNAD TGLIDYDEVE QLAKAHRPKL IIAGFTAYSR 

       190        200        210        220        230        240 
IVDWQRFRAI ADGVGAYLLA DIAHLAGMIA AGIYPNPVQI ADVTTSTTHK TLRGPRSGLI 

       250        260        270        280        290        300 
LAKANPEIEK KLNSKVFPGI QGGPLMHVVA AKAVAFKEAM EPAFKDYQRQ VIRNAQAMAE 

       310        320        330        340        350        360 
AIQSRGYKIV SGGTDSHLFL VDLVAKGLTG KAADAALGRA NITVNKNTVP NDPQSPFVTS 

       370        380        390        400        410 
GIRIGSPAMT TRGFKEAEIC ELAGWVCDVL DDIENETVIA DTKEKVLALC ARFPVYG

« Hide

References

[1]"Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707."
Klotz M.G., Arp D.J., Chain P.S.G., El-Sheikh A.F., Hauser L.J., Hommes N.G., Larimer F.W., Malfatti S.A., Norton J.M., Poret-Peterson A.T., Vergez L.M., Ward B.B.
Appl. Environ. Microbiol. 72:6299-6315(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 19707 / NCIMB 11848.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP000127 Genomic DNA. Translation: ABA58488.1.
RefSeqYP_344018.1. NC_007484.1.

3D structure databases

ProteinModelPortalQ3J9K8.
SMRQ3J9K8. Positions 1-417.
ModBaseSearch...

Protein-protein interaction databases

STRING323261.Noc_2027.

Proteomic databases

PRIDEQ3J9K8.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABA58488; ABA58488; Noc_2027.
GeneID3705178.
KEGGnoc:Noc_2027.
PATRIC22708366. VBINitOce57959_2398.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0112.
HOGENOMHOG000239404.
KOK00600.
OMAIAKLQWA.
ProtClustDBCLSK2771466.

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_NITOC
AccessionPrimary (citable) accession number: Q3J9K8
Entry history
Integrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: November 8, 2005
Last modified: May 1, 2013
This is version 59 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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