Q0IDD8 (GLYA_SYNS3) Reviewed, UniProtKB/Swiss-Prot

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:	sync_0300

Organism

Synechococcus sp. (strain CC9311) [Complete proteome] [HAMAP]

Taxonomic identifier

64471 [NCBI]

Taxonomic lineage

Bacteria › Cyanobacteria › Chroococcales › Synechococcus

Protein attributes

Sequence length	429 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 – 429	429	Pyridoxal-phosphate-dependent serine hydroxymethyltransferase		PRO_1000006339
Regions
	Region	130 – 132	3	Substrate binding By similarity
Sites
	Binding site	40	1	Pyridoxal phosphate By similarity
	Binding site	60	1	Pyridoxal phosphate By similarity
	Binding site	62	1	Substrate By similarity
	Binding site	69	1	Substrate binding By similarity
	Binding site	70	1	Pyridoxal phosphate By similarity
	Binding site	126	1	Substrate By similarity
	Binding site	181	1	Pyridoxal phosphate By similarity
	Binding site	209	1	Pyridoxal phosphate By similarity
	Binding site	234	1	Pyridoxal phosphate By similarity
	Binding site	241	1	Pyridoxal phosphate By similarity
	Binding site	267	1	Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen By similarity
	Binding site	367	1	Pyridoxal phosphate By similarity
Amino acid modifications
	Modified residue	235	1	N6-(pyridoxal phosphate)lysine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q0IDD8 [UniParc]. Last modified October 3, 2006. Version 1. Checksum: AAD67F3BFD82EFF8	FASTA	429	46,185
	10 20 30 40 50 60 MTDRSAAPIN ASLKAADPAI AGLIDQEQMR QETHLELIAS ENFTSKAVME AQGSVLTNKY 70 80 90 100 110 120 AEGLPHKRYY GGCEHVDAIE ELAITRAKQL FGAAWANVQP HSGAQANFAV FLALLQPGDT 130 140 150 160 170 180 ILGMDLSHGG HLTHGSPVNV SGKWFNVVQY GVDKETQRLD MEAIRKLALE HKPKLIICGY 190 200 210 220 230 240 SAYPRSIDFA AFRSIADEVG AYLLADMAHI AGLVAAGVHA SPVPHCDVVT TTTHKTLRGP 250 260 270 280 290 300 RGGLILCRDA EFARRFDKAV FPGSQGGPLE HVIAAKAVAF GEALQPDFKA YSRQVVANAQ 310 320 330 340 350 360 ALAARLQERK IDVVSGGTDN HVVLLDLRSI GMTGKVADLL VSDVHITANK NTVPFDPESP 370 380 390 400 410 420 FVTSGLRLGT AALTTRGFDE KAFHEVADVI ADRLQNPEDD AIQARCLERV SDLCKRFPLY APALEPALA

References

[1]

"Genome sequence of Synechococcus CC9311: insights into adaptation to a coastal environment." Palenik B., Ren Q., Dupont C.L., Myers G.S., Heidelberg J.F., Badger J.H., Madupu R., Nelson W.C., Brinkac L.M., Dodson R.J., Durkin A.S., Daugherty S.C., Sullivan S.A., Khouri H., Mohamoud Y., Halpin R., Paulsen I.T. Proc. Natl. Acad. Sci. U.S.A. 103:13555-13559(2006) [PubMed: 16938853] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CC9311.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000435 Genomic DNA. Translation: ABI46562.1.
RefSeq	YP_729534.1. NC_008319.1.
3D structure databases
ProteinModelPortal	Q0IDD8.
SMR	Q0IDD8. Positions 13-413.
ModBase	Search...
Protein-protein interaction databases
STRING	Q0IDD8.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	4259129.
GenomeReviews	Gene locus sync_0300 in contig CP000435_GR.
KEGG	syg:sync_0300.
PATRIC	23791454. VBISynSp88089_0309.
TIGR	sync_0300.
Phylogenomic databases
eggNOG	COG0112.
HOGENOM	HBG301263.
OMA	GTSNHLM.
PhylomeDB	Q0IDD8.
ProtClustDB	PRK00011.
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_SYNS3

Accession

Primary (citable) accession number: Q0IDD8

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	October 3, 2006
Last modified:	January 25, 2012
This is version 41 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program