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B3EMW0 (GLYA_CHLPB) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 41. 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:Cphamn1_0630
OrganismChlorobium phaeobacteroides (strain BS1) [Complete proteome] [HAMAP]
Taxonomic identifier331678 [NCBI]
Taxonomic lineageBacteria › Chlorobi › Chlorobia › Chlorobiales › Chlorobiaceae › Chlorobium/Pelodictyon group › Chlorobium ›

Protein attributes

Sequence length439 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.

Sequence caution

The sequence ACE03588.1 differs from that shown. Reason: Erroneous initiation.

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 – 439439Serine hydroxymethyltransferase HAMAP-Rule MF_00051
PRO_0000369907

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
B3EMW0 [UniParc].

Last modified April 14, 2009. Version 2.
Checksum: D1608C5C0D311A10

FASTA43947,691
        10         20         30         40         50         60 
MNMDILQRQD KGIFDAITAE VRRQTETLEL IASENFASRA VMEACGSVMT NKYAEGYPGK 

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

       130        140        150        160        170        180 
HGGHLTHGSK VNFSGQLFEA HSYGVDRETG CIDMNKVEEM ALEVRPKLII CGASAYSQGF 

       190        200        210        220        230        240 
DFKAFRDVAD KVGAFLMADI AHPAGLIAAG LLNDPMPHCH FVTTTTHKTL RGPRGGMIMM 

       250        260        270        280        290        300 
GKDFENPLGI TVKTKKGSRT KMMSEVIDAE IMPGIQGGPL MHIIAAKGVA FGEALQPEFK 

       310        320        330        340        350        360 
DYAVQVRNNA AVMAERFSGL DYQIVSGGTK NHLMLIDLRN KNVTGKVAEN LLHDAGITVN 

       370        380        390        400        410        420 
KNMVPFDDKS PFVTSGIRIG TPAMTTRGMQ ESHAENIVGF IDRVISAADS EGIEKVCAEV 

       430 
RSDVKAMCKD LPLNDFGPE

« Hide

References

[1]"Complete sequence of Chlorobium phaeobacteroides BS1."
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., Ovchinnikova G., Li T., Liu Z., 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: BS1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP001101 Genomic DNA. Translation: ACE03588.1. Different initiation.
RefSeqYP_001959069.1. NC_010831.1.

3D structure databases

ProteinModelPortalB3EMW0.
ModBaseSearch...

Protein-protein interaction databases

STRING331678.Cphamn1_0630.

Proteomic databases

PRIDEB3EMW0.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACE03588; ACE03588; Cphamn1_0630.
GeneID6374294.
KEGGcpb:Cphamn1_0630.
PATRIC21383330. VBIChlPha121022_0675.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0112.
HOGENOMHOG000239404.
KOK00600.
OMAMMSEVID.
ProtClustDBPRK00011.

Enzyme and pathway databases

BioCycCPHA331678:GHME-652-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_CHLPB
AccessionPrimary (citable) accession number: B3EMW0
Entry history
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: April 14, 2009
Last modified: May 1, 2013
This is version 41 of the entry and version 2 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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