Pyridoxal-phosphate-dependent serine hydroxymethyltransferase - Lactococcus lactis subsp. cremoris (strain MG1363)

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A2RIS0 (GLYA_LACLM) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 38. 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:	llmg_0563

Organism

Lactococcus lactis subsp. cremoris (strain MG1363) [Complete proteome] [HAMAP]

Taxonomic identifier

Taxonomic lineage

Bacteria › Firmicutes › Lactobacillales › Streptococcaceae › Lactococcus

Protein attributes

Sequence length	415 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

415

Pyridoxal-phosphate-dependent serine hydroxymethyltransferase

PRO_1000006271

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

A2RIS0 [UniParc].

Last modified March 6, 2007. Version 1.
Checksum: 04963A7EA5124F9D
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415

44,823

        10         20         30         40         50         60 
MIFDKEDFES FDPELWAAIH AEEIRQQQNI ELIASENIVS KAVMAAQGSV LTNKYAEGYP 

        70         80         90        100        110        120 
GKRYYGGTEA VDVVENLAID RAKELFGAKF ANVQPHSGSQ ANAAAYMALI QPGDTVLGMD 

       130        140        150        160        170        180 
LNAGGHLTHG ASVNFSGKTY HFVPYGVNPQ TELLDYEEIL KIAKEVQPKL IVAGASAYSR 

       190        200        210        220        230        240 
LIDFAKFRQI ADSVGAKLMV DMAHIAGLVA TGAHPNPLPY ADVVTTTTHK TLRGPRGGMI 

       250        260        270        280        290        300 
LTNDEVLAKK INSAIFPGTQ GGPLEHVIAA KAVAFKEALD PEFATYIEQV IKNTQAMADE 

       310        320        330        340        350        360 
FAKVDGLRLI AGGSDNHLLN LKVLDLGING KEAQDLLDSV HITLNKEAIP DETLSPFKTS 

       370        380        390        400        410 
GVRIGAAAIT SRGFKEAEAR KVAQLVSKAL VNHDNQEKLE EVRKSALELT HQFPL

References

[1]

"The complete genome sequence of the lactic acid bacterial paradigm Lactococcus lactis subsp. cremoris MG1363."
Wegmann U., O'Connell-Motherway M., Zomer A., Buist G., Shearman C., Canchaya C., Ventura M., Goesmann A., Gasson M.J., Kuipers O.P., van Sinderen D., Kok J.
J. Bacteriol. 189:3256-3270(2007) [PubMed: 17307855] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: MG1363.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AM406671 Genomic DNA. Translation: CAL97165.1.
RefSeq	YP_001031911.1. NC_009004.1.
3D structure databases
ProteinModelPortal	A2RIS0.
SMR	A2RIS0. Positions 12-414.
ModBase	Search...
Protein-protein interaction databases
STRING	A2RIS0.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	4798116.
GenomeReviews	Gene locus llmg_0563 in contig AM406671_GR.
KEGG	llm:llmg_0563.
PATRIC	22282213. VBILacLac4574_0574.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0112.
HOGENOM	HBG301263.
OMA	CNKNMIP.
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_LACLM

Accession

Primary (citable) accession number: A2RIS0

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	March 6, 2007
Last modified:	January 25, 2012
This is version 38 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