Pyridoxal-phosphate-dependent serine hydroxymethyltransferase - Janthinobacterium sp. (strain Marseille)

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A6T0T6 (GLYA_JANMA) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 34. History...

Clusters with 100%, 90%, 50% identity |

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Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Pyridoxal-phosphate-dependent serine hydroxymethyltransferase
Short name=SHMT
Short name=Serine methylase
EC=2.1.2.1

Gene names

Name:	glyA
Ordered Locus Names:	mma_2443

Organism

Janthinobacterium sp. (strain Marseille) (Minibacterium massiliensis) [Complete proteome] [HAMAP]

Taxonomic identifier

Taxonomic lineage

Bacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › Oxalobacteraceae › Janthinobacterium

Protein attributes

Sequence length	414 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate serving as the one-carbon carrier By similarity.
Catalytic activity	5,10-methylenetetrahydrofolate + glycine + H₂O = tetrahydrofolate + L-serine. HAMAP MF_00051
Cofactor	Pyridoxal phosphate By similarity. HAMAP MF_00051
Pathway	One-carbon metabolism; tetrahydrofolate interconversion. HAMAP MF_00051 Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1.
Subunit structure	Homodimer By similarity.
Subcellular location	Cytoplasm By similarity HAMAP MF_00051.
Sequence similarities	Belongs to the SHMT family.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis One-carbon metabolism
Cellular component	Cytoplasm
Ligand	Pyridoxal phosphate
Molecular function	Transferase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	L-serine metabolic process Inferred from electronic annotation. Source: InterPro glycine metabolic process Inferred from electronic annotation. Source: InterPro one-carbon metabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	glycine hydroxymethyltransferase activity Inferred from electronic annotation. Source: EC pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

414

Pyridoxal-phosphate-dependent serine hydroxymethyltransferase

PRO_1000006266

Regions

Region

3

Substrate binding By similarity

Sites

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Substrate By similarity

Binding site

1

Substrate binding By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Substrate By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen By similarity

Binding site

1

Pyridoxal phosphate By similarity

Amino acid modifications

Modified residue

1

N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

A6T0T6 [UniParc].

Last modified August 21, 2007. Version 1.
Checksum: C43145039A12513B
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414

45,138

        10         20         30         40         50         60 
MFSKDQTLAK TDAELWSAIQ KENTRQQEHI ELIASENYTS PAVMEAQGTQ LTNKYAEGYP 

        70         80         90        100        110        120 
GKRYYGGCEY VDIVEQLAID RLKQLYGADA ANVQPNSGSQ ANQGVFLAVL KPGDTIMGMS 

       130        140        150        160        170        180 
LAEGGHLTHG MALNMSGKWF NVVSYGLNDK EEIDYDAMER LAREHKPKLI IAGASAYALR 

       190        200        210        220        230        240 
IDFERFAKIA KEIGAYFMVD MAHYAGLIAA GEYPNPVPFA DFVTSTTHKS LRGPRGGFIL 

       250        260        270        280        290        300 
MKAEHEKIIN SAIFPGLQGG PLMHVIAGKA VAFKEALAPE FKTYQQQVVK NADALAKALI 

       310        320        330        340        350        360 
ARGLRIVSNR TESHVMLVDL RAKKITGKDA ENLLGSAHIT CNKNAIPNDP EKPFVTSGIR 

       370        380        390        400        410 
LGSPAMTTRG FKEAEATKVG NLIADVLENP NDAATIERVK AEVKKLTDAF PVYG

References

[1]

"Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria."
Audic S., Robert C., Campagna B., Parinello H., Claverie J.-M., Raoult D., Drancourt M.
PLoS Genet. 3:1454-1463(2007) [PubMed: 17722982] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Marseille.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000269 Genomic DNA. Translation: ABR88534.1.
RefSeq	YP_001354133.1. NC_009659.1.
3D structure databases
ProteinModelPortal	A6T0T6.
SMR	A6T0T6. Positions 1-414.
ModBase	Search...
Protein-protein interaction databases
STRING	A6T0T6.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	5350815.
GenomeReviews	Gene locus mma_2443 in contig CP000269_GR.
KEGG	mms:mma_2443.
PATRIC	22157381. VBIJanSp106498_2456.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0112.
HOGENOM	HBG301263.
OMA	RIDFERI.
ProtClustDB	PRK00011.
Enzyme and pathway databases
BioCyc	JSP375286:MMA_2443-MONOMER.
Family and domain databases
HAMAP	MF_00051. SHMT. [Tree]
InterPro	IPR015424. PyrdxlP-dep_Trfase_major_dom. IPR015421. PyrdxlP-dep_Trfase_major_sub1. IPR015422. PyrdxlP-dep_Trfase_major_sub2. IPR001085. Ser_HO-MeTrfase. IPR019798. Ser_HO-MeTrfase_PLP_BS. [Graphical view]
Gene3D	G3DSA:3.40.640.10. PyrdxlP-dep_Trfase_major_sub1. 1 hit. G3DSA:3.90.1150.10. PyrdxlP-dep_Trfase_major_sub2. 1 hit.
KO	K00600.
PANTHER	PTHR11680. Gly_HO-Metrfase. 1 hit.
Pfam	PF00464. SHMT. 1 hit. [Graphical view]
PIRSF	PIRSF000412. SHMT. 1 hit.
SUPFAM	SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.
PROSITE	PS00096. SHMT. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

GLYA_JANMA

Accession

Primary (citable) accession number: A6T0T6

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	August 21, 2007
Last modified:	January 25, 2012
This is version 34 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic 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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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents