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B5E8U0 (GLYA_GEOBB) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 38. 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:Gbem_3102
OrganismGeobacter bemidjiensis (strain Bem / ATCC BAA-1014 / DSM 16622) [Complete proteome] [HAMAP]
Taxonomic identifier404380 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Deltaproteobacteria › Desulfuromonadales › Geobacteraceae › Geobacter ›

Protein attributes

Sequence length415 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 – 415415Serine hydroxymethyltransferase HAMAP-Rule MF_00051
PRO_1000091543

Regions

Region121 – 1233Substrate binding By similarity
Region349 – 3513Substrate binding By similarity

Sites

Binding site311Pyridoxal phosphate By similarity
Binding site511Pyridoxal phosphate By similarity
Binding site531Substrate By similarity
Binding site601Substrate By similarity
Binding site611Pyridoxal phosphate By similarity
Binding site951Pyridoxal phosphate By similarity
Binding site1171Substrate; via carbonyl oxygen By similarity
Binding site1721Pyridoxal phosphate By similarity
Binding site2001Pyridoxal phosphate By similarity
Binding site2251Pyridoxal phosphate By similarity
Binding site2321Pyridoxal phosphate By similarity
Binding site2571Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen By similarity
Binding site3571Pyridoxal phosphate By similarity

Amino acid modifications

Modified residue2261N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence LengthMass (Da)Tools
B5E8U0 [UniParc].

Last modified October 14, 2008. Version 1.
Checksum: 72283D4255C7D5E5

FASTA41544,925
        10         20         30         40         50         60 
MSVLETFDPA VAEVIRQETE RQEYNLELIA SENFVSPAVL EAQGSVLTNK YAEGYPGKRY 

        70         80         90        100        110        120 
YGGCHCVDVV ENLAIDRAKE LFGADHVNVQ PHSGSQANMA VYFSVLKPGD TVLGMNLAHG 

       130        140        150        160        170        180 
GHLTHGSPVN FSGKLFNIVP YGVSKETQTI DYEETERLAL EHKPKMIVVG ASAYPRIIDF 

       190        200        210        220        230        240 
EAFRRIADKV GAVVMVDMAH IAGLVAAGLH PSPVPYAEFV TTTTHKTLRG PRGGMIMCRE 

       250        260        270        280        290        300 
DWAKTLNSNI FPGIQGGPLM HVIAAKAVAF KEALTPEFKQ YQGQIVKNAK ALAEGLTKRG 

       310        320        330        340        350        360 
FKLTSGGTDN HLMLVDLSQT ELTGKVAEEA LDRAGITVNK NGIPFDTRSP FITSGIRIGT 

       370        380        390        400        410 
PAATSHGLKE AEMEQVAGFI AEVLGNVSDE AKLAAVKTQV NALMKRFPMY ANRLV

« Hide

References

[1]"Complete sequence of Geobacter bemidjiensis BEM."
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., Kiss H., Brettin T., Detter J.C., Han C., Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L. expand/collapse author list , Kyrpides N., Lykidis A., Lovley D., Richardson P.
Submitted (JUL-2008) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Bem / ATCC BAA-1014 / DSM 16622.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP001124 Genomic DNA. Translation: ACH40104.1.
RefSeqYP_002139900.1. NC_011146.1.

3D structure databases

ProteinModelPortalB5E8U0.
SMRB5E8U0. Positions 1-403.
ModBaseSearch...

Protein-protein interaction databases

STRING404380.Gbem_3102.

Proteomic databases

PRIDEB5E8U0.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACH40104; ACH40104; Gbem_3102.
GeneID6779961.
KEGGgbm:Gbem_3102.
PATRIC21989838. VBIGeoBem56306_3028.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0112.
HOGENOMHOG000239405.
KOK00600.
OMADYEETER.
ProtClustDBPRK00011.

Enzyme and pathway databases

BioCycGBEM404380:GHFR-3167-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_GEOBB
AccessionPrimary (citable) accession number: B5E8U0
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: October 14, 2008
Last modified: May 1, 2013
This is version 38 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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