Q46HB6 (GLYA_PROMT) 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:	PMN2A_1624

Organism

Prochlorococcus marinus (strain NATL2A) [Complete proteome] [HAMAP]

Taxonomic identifier

59920 [NCBI]

Taxonomic lineage

Bacteria › Cyanobacteria › Prochlorophytes › Prochlorococcaceae › Prochlorococcus

Protein attributes

Sequence length	411 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 – 411	411	Pyridoxal-phosphate-dependent serine hydroxymethyltransferase		PRO_0000234999
Regions
	Region	117 – 119	3	Substrate binding By similarity
Sites
	Binding site	27	1	Pyridoxal phosphate By similarity
	Binding site	47	1	Pyridoxal phosphate By similarity
	Binding site	49	1	Substrate By similarity
	Binding site	56	1	Substrate binding By similarity
	Binding site	57	1	Pyridoxal phosphate By similarity
	Binding site	113	1	Substrate By similarity
	Binding site	168	1	Pyridoxal phosphate By similarity
	Binding site	196	1	Pyridoxal phosphate By similarity
	Binding site	221	1	Pyridoxal phosphate By similarity
	Binding site	228	1	Pyridoxal phosphate By similarity
	Binding site	254	1	Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen By similarity
	Binding site	354	1	Pyridoxal phosphate By similarity
Amino acid modifications
	Modified residue	222	1	N6-(pyridoxal phosphate)lysine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q46HB6 [UniParc]. Last modified September 13, 2005. Version 1. Checksum: D3169D5EBFFB0410	FASTA	411	44,723
	10 20 30 40 50 60 MKCDPSIAKL INNELSRQET HLELIASENF ASKAVMEAQG SVLTNKYAEG LPNKRYYGGC 70 80 90 100 110 120 EYVDGVEQLA IDRAKNLFGA NWANVQPHSG AQANFAVFLS LLKPGDTIMG MDLSHGGHLT 130 140 150 160 170 180 HGSPVNVSGK WFKTCHYEVD KKTEMLDMDA IRKKAIENQP KLIICGFSAY PRKIDFKAFR 190 200 210 220 230 240 SIADEVNAYL LADIAHIAGL VASGLHPSPI PYCDVVTTTT HKTLRGPRGG LILSKDKEIG 250 260 270 280 290 300 KKLDKAVFPG TQGGPLEHVI AAKAVAFKEA SAPEFKIYSQ KVISNAKVLS NQLQKRGISI 310 320 330 340 350 360 VSKGTDNHIV LLDLRSIGMT GKVADQLVSD IKITANKNTV PFDPESPFVT SGLRLGSAAL 370 380 390 400 410 TTRGFNEQAF GDVGNVIADR LLNPNDEDIK EKSINKVSEL CNKFPLYSEN I

References

[1]

"Patterns and implications of gene gain and loss in the evolution of Prochlorococcus." Kettler G.C., Martiny A.C., Huang K., Zucker J., Coleman M.L., Rodrigue S., Chen F., Lapidus A., Ferriera S., Johnson J., Steglich C., Church G.M., Richardson P., Chisholm S.W. PLoS Genet. 3:2515-2528(2007) [PubMed: 18159947] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: NATL2A.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000095 Genomic DNA. Translation: AAZ59112.1.
RefSeq	YP_292815.1. NC_007335.2.
3D structure databases
ProteinModelPortal	Q46HB6.
SMR	Q46HB6. Positions 2-392.
ModBase	Search...
Protein-protein interaction databases
STRING	Q46HB6.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	3607023.
GenomeReviews	Gene locus PMN2A_1624 in contig CP000095_GR.
KEGG	pmn:PMN2A_1624.
PATRIC	23022731. VBIProMar14922_0323.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0112.
HOGENOM	HBG301263.
OMA	NRGINIV.
PhylomeDB	Q46HB6.
ProtClustDB	PRK00011.
Enzyme and pathway databases
BioCyc	PMAR59920:PMN2A_1624-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_PROMT

Accession

Primary (citable) accession number: Q46HB6

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 16, 2006
Last sequence update:	September 13, 2005
Last modified:	January 25, 2012
This is version 45 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program