Q87I03 (GLYA2_VIBPA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Pyridoxal-phosphate-dependent serine hydroxymethyltransferase 2
Short name=SHMT 2
Short name=Serine methylase 2
EC=2.1.2.1

Gene names

Name:	glyA2
Ordered Locus Names:	VPA0803

Organism

Vibrio parahaemolyticus [Complete proteome] [HAMAP]

Taxonomic identifier

670 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio

Protein attributes

Sequence length	431 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	1 – 431	431	Pyridoxal-phosphate-dependent serine hydroxymethyltransferase 2		PRO_0000113693
Regions
	Region	135 – 137	3	Substrate binding By similarity
Sites
	Binding site	45	1	Pyridoxal phosphate By similarity
	Binding site	65	1	Pyridoxal phosphate By similarity
	Binding site	67	1	Substrate By similarity
	Binding site	74	1	Substrate binding By similarity
	Binding site	75	1	Pyridoxal phosphate By similarity
	Binding site	131	1	Substrate By similarity
	Binding site	186	1	Pyridoxal phosphate By similarity
	Binding site	214	1	Pyridoxal phosphate By similarity
	Binding site	239	1	Pyridoxal phosphate By similarity
	Binding site	246	1	Pyridoxal phosphate By similarity
	Binding site	272	1	Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen By similarity
	Binding site	372	1	Pyridoxal phosphate By similarity
Amino acid modifications
	Modified residue	240	1	N6-(pyridoxal phosphate)lysine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q87I03 [UniParc]. Last modified May 23, 2003. Version 1. Checksum: CC0A30799E80C6E7	FASTA	431	46,507
	10 20 30 40 50 60 MNKSYPNHSL ENFFSTNLSA TDDAVFAGIQ AEFTRQNEQI ELIASENIVS KAVMQAQGTC 70 80 90 100 110 120 LTNKYAEGYP GRRYYGGCEH VDTVEAIAIE RAKKLFNCEY ANVQPHSGAQ ANGAVKLALL 130 140 150 160 170 180 QPGDTILGMS LDAGGHLTHG ARPALSGKWF NAVQYGVDRE TLEINYDDVR ALALEHKPKM 190 200 210 220 230 240 IIAGGSAIPR TIDFAKFREI ADEVNAILMV DMAHIAGLIA TGAHPSPLPH AHVVTTTTHK 250 260 270 280 290 300 TLRGPRGGMI LTNHEDIIKK INSAVFPGLQ GGPLMHVIAA KAVAFGEALG PEFKTYIDSV 310 320 330 340 350 360 INNAKVLAEV LQTRGCDIVT GGTDTHLMLV DLRPKGLKGN KAEEALERAG ITCNKNGIPF 370 380 390 400 410 420 DTEKPMITSG IRLGTPAGTS RGFGAEEFKL IGNWIGDVLD GLVNNPEGDA IVEKRVRKEV 430 KELCSRFPLY Q

References

[1]

"Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae." Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T. Lancet 361:743-749(2003) [PubMed: 12620739] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: RIMD 2210633 / Serotype O3:K6.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000032 Genomic DNA. Translation: BAC62146.1.
RefSeq	NP_800313.1. NC_004605.1.
3D structure databases
ProteinModelPortal	Q87I03.
SMR	Q87I03. Positions 18-399.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1191492.
GenomeReviews	Gene locus VPA0803 in contig BA000032_GR.
KEGG	vpa:VPA0803.
NMPDR	fig|223926.1.peg.3883.
PATRIC	20146003. VBIVibPar50997_3734.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG301263.
OMA	MILTNHE.
ProtClustDB	PRK13034.
Enzyme and pathway databases
BioCyc	VPAR223926:VPA0803-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

GLYA2_VIBPA

Accession

Primary (citable) accession number: Q87I03

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 23, 2003
Last sequence update:	May 23, 2003
Last modified:	January 25, 2012
This is version 59 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program