Serine hydroxymethyltransferase - Bradyrhizobium japonicum (strain USDA 110)

Contribute

Read comments (?) or add your own

P24060 (GLYA_BRAJA) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 99. History...

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

Documents (2) |

Third-party data

text xml rdf/xml gff fasta

to top of page

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

to top of page

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

Names and origin

Protein names

Recommended name:
Serine hydroxymethyltransferase
Short name=SHMT
Short name=Serine methylase
EC=2.1.2.1

Gene names

Name:	glyA
Ordered Locus Names:	bll5033

Organism

Bradyrhizobium japonicum (strain USDA 110) [Reference proteome] [HAMAP]

Taxonomic identifier

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Bradyrhizobiaceae › Bradyrhizobium ›

Protein attributes

Sequence length	432 AA.
Sequence status	Complete.
Protein existence	Inferred 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.
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 process	Amino-acid biosynthesis One-carbon metabolism
Cellular component	Cytoplasm
Ligand	Pyridoxal phosphate
Molecular function	Transferase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	glycine biosynthetic process from serine Inferred from electronic annotation. Source: HAMAP tetrahydrofolate interconversion Inferred from electronic annotation. Source: UniProtKB-UniPathway
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	glycine hydroxymethyltransferase activity Inferred from electronic annotation. Source: HAMAP pyridoxal phosphate binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

432

Serine hydroxymethyltransferase HAMAP-Rule MF_00051

PRO_0000113544

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 By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Substrate; via carbonyl oxygen 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

Experimental info

Sequence conflict

1

R → L in CAA38450. Ref.1

Sequences

Sequence

Length

Mass (Da)

Tools

P24060 [UniParc].

Last modified February 28, 2003. Version 2.
Checksum: 2D3F6EA0F0D2A235
Show »

432

46,035

        10         20         30         40         50         60 
MTSAKTASAP DSFFTASLDQ ADPEIAAAIK GELGRQRHEV ELIASENIVS RAVLEAQGSV 

        70         80         90        100        110        120 
MTNKYAEGYP GARYYGGCEW VDVAENLAID RAKKLFGAGF ANVQPNSGSQ MNQAVFLALL 

       130        140        150        160        170        180 
QPGDTFMGLD LAAGGHLTHG SPVNMSGKWF KAAHYTVRRE DQIIDMDAVQ KQAEEIKPKL 

       190        200        210        220        230        240 
IVAGGSAYSR AWDFKRFREI ADSVGAYLLV DMAHFAGLVA GGVHASPVPY AHVTTTTTHK 

       250        260        270        280        290        300 
SLRGPRGGLI LSNDETLAKK LNSAIFPGLQ GGPLMHVIAA KAVAFGEALR PDFKVYAKNV 

       310        320        330        340        350        360 
VENAKALAEA MKSHGFDIVS GGTDNHLMLV DLRPKGLKGN VSEKALVRAA ITCNKNGIPF 

       370        380        390        400        410        420 
DPEKPFVTSG LRLGTPAATT RGFGVAEFQQ VGGMIAEVLN AIAQSDDGKA PLVEAAIKER 

       430 
VKALTDRFPI YQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of glyA as a symbiotically essential gene in Bradyrhizobium japonicum." Rossbach S., Hennecke H. Mol. Microbiol. 5:39-47(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: USDA 110spc4.
[2]	"Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110." Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S., Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M., Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S. DNA Res. 9:189-197(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: USDA 110.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X54638 Genomic DNA. Translation: CAA38450.1. BA000040 Genomic DNA. Translation: BAC50298.1.
PIR	S15203.
RefSeq	NP_771673.1. NC_004463.1.
3D structure databases
ProteinModelPortal	P24060.
SMR	P24060. Positions 18-426.
ModBase	Search...
Protein-protein interaction databases
STRING	224911.bll5033.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	BAC50298; BAC50298; BAC50298.
GeneID	1051853.
KEGG	bja:bll5033.
PATRIC	21193730. VBIBraJap65052_5110.
Phylogenomic databases
eggNOG	COG0112.
HOGENOM	HOG000239404.
KO	K00600.
OMA	IFGAIGK.
ProtClustDB	PRK00011.
Enzyme and pathway databases
BioCyc	BJAP224911:GJEJ-5070-MONOMER.
UniPathway	UPA00193. UPA00288; UER01023.
Family and domain databases
Gene3D	3.40.640.10. 1 hit. 3.90.1150.10. 1 hit.
HAMAP	MF_00051. SHMT.
InterPro	IPR015424. 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]
PANTHER	PTHR11680. PTHR11680. 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_BRAJA

Accession

Primary (citable) accession number: P24060

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 1992
Last sequence update:	February 28, 2003
Last modified:	May 1, 2013
This is version 99 of the entry and version 2 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

to top of page

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