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P56990 (GLYA_NEIMB) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 89. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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:NMB1055
OrganismNeisseria meningitidis serogroup B (strain MC58) [Reference proteome] [HAMAP]
Taxonomic identifier122586 [NCBI]
Taxonomic lineageBacteriaProteobacteriaBetaproteobacteriaNeisserialesNeisseriaceaeNeisseria

Protein attributes

Sequence length416 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
Reference proteome
Gene Ontology (GO)
   Biological_processglycine biosynthetic process from serine

Inferred from electronic annotation. Source: UniProtKB-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: UniProtKB-HAMAP

pyridoxal phosphate binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 416416Serine hydroxymethyltransferase HAMAP-Rule MF_00051
PRO_0000113623

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 site991Pyridoxal 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 site2611Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen By similarity
Binding site3611Pyridoxal phosphate By similarity

Amino acid modifications

Modified residue2291N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence LengthMass (Da)Tools
P56990 [UniParc].

Last modified December 1, 2000. Version 1.
Checksum: 393E4BBF7825921C

FASTA41644,916
        10         20         30         40         50         60 
MFSKSVTLAQ YDPDLAAAIA QEDQRQQDHV ELIASENYVS CAVMDAQGSQ LTNKYAEGYP 

        70         80         90        100        110        120 
GKRYYGGCEY VDIVEQLAID RVKELFGAAY ANVQPHSGSQ ANQAVYASVL KPGDTILGMS 

       130        140        150        160        170        180 
LAHGGHLTHG ASVNISGKLY NAVTYGLDEN EVLDYAEVER LALEHKPKMI VAGASAYALQ 

       190        200        210        220        230        240 
IDWAKFREIA DKVGAYLFVD MAHYAGLVAG GEYPNPVPFC DFVTTTTHKT LRGPRGGVIL 

       250        260        270        280        290        300 
CRDNTHEKAL NSSIFPSLQG GPLMHVIAAK AVAFKEALQP EFKQYAKQVK INAAAMAEEL 

       310        320        330        340        350        360 
VKRGLRIVSG RTESHVFLVD LQPMKITGKA AEAALGKAHI TVNKNAIPND PEKPFVTSGI 

       370        380        390        400        410 
RIGSAAMTTR GFNEADARVL ANLVADVLSN PEDEANLAKV RKQVTALCNK YPVYGA 

« Hide

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE002098 Genomic DNA. Translation: AAF41452.1.
PIRB81126.
RefSeqNP_274089.1. NC_003112.2.

3D structure databases

ProteinModelPortalP56990.
SMRP56990. Positions 1-415.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING122586.NMB1055.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAF41452; AAF41452; NMB1055.
GeneID903374.
KEGGnme:NMB1055.
PATRIC20357651. VBINeiMen85645_1342.

Phylogenomic databases

eggNOGCOG0112.
HOGENOMHOG000239404.
KOK00600.
OMANGTDSHM.
OrthoDBEOG6Z0QB2.
ProtClustDBPRK00011.

Enzyme and pathway databases

BioCycNMEN122586:GHGG-1092-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. SSF53383. 1 hit.
PROSITEPS00096. SHMT. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameGLYA_NEIMB
AccessionPrimary (citable) accession number: P56990
Entry history
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: December 1, 2000
Last modified: February 19, 2014
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways