Pyridoxal-phosphate-dependent serine hydroxymethyltransferase - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)

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Q04KR0 (GLYA_STRP2) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 38. History...

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

Documents (2) |

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:	SPD_0910

Organism

Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) [Complete proteome] [HAMAP]

Taxonomic identifier

Taxonomic lineage

Bacteria › Firmicutes › Lactobacillales › Streptococcaceae › Streptococcus

Protein attributes

Sequence length	418 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

418

Pyridoxal-phosphate-dependent serine hydroxymethyltransferase

PRO_1000006327

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

Q04KR0 [UniParc].

Last modified November 14, 2006. Version 1.
Checksum: 97D07D488FDF8250
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418

45,256

        10         20         30         40         50         60 
MIFDKDDFKA YDADLWNAIA KEEERQQNNI ELIASENVVS KAVMAAQGSI LTNKYAEGYP 

        70         80         90        100        110        120 
GRRYYGGTDV VDVVETLAIE RAKEIFGAKF ANVQPHSGSQ ANCAAYMSLI EPGDTVMGMD 

       130        140        150        160        170        180 
LAAGGHLTHG APVSFSGQTY NFLSYSVDPE TELLDFDAIL KQAQEVKPKL IVAGASAYSQ 

       190        200        210        220        230        240 
IIDFSKFREI ADAVGAKLMV DMAHIAGLVA AGLHPSPVPY AHITTTTTHK TLRGPRGGLI 

       250        260        270        280        290        300 
LTNDEELAKK INSAIFPGIQ GGPLEHVVAA KAVSFKEVLD PAFKEYAANV IKNSKAMADV 

       310        320        330        340        350        360 
FLQDPDFRII SGGTENHLFL VDVTKVVENG KVAQNLLDEV NITLNKNSIP YETLSPFKTS 

       370        380        390        400        410 
GIRIGAAAIT ARGFGEEESR KVAELIIKTL KNSENEAVLE EVRSAVKELT DAFPLYED

References

[1]

"Genome sequence of Avery's virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6."
Lanie J.A., Ng W.-L., Kazmierczak K.M., Andrzejewski T.M., Davidsen T.M., Wayne K.J., Tettelin H., Glass J.I., Winkler M.E.
J. Bacteriol. 189:38-51(2007) [PubMed: 17041037] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: D39 / NCTC 7466.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000410 Genomic DNA. Translation: ABJ55301.1.
RefSeq	YP_816388.1. NC_008533.1.
3D structure databases
ProteinModelPortal	Q04KR0.
ModBase	Search...
Protein-protein interaction databases
STRING	Q04KR0.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	EBSTRT00000019709; EBSTRP00000018949; EBSTRG00000019709.
GeneID	4441989.
GenomeReviews	Gene locus SPD_0910 in contig CP000410_GR.
KEGG	spd:SPD_0910.
PATRIC	19682971. VBIStrPne27904_1021.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0112.
GeneTree	EBGT00050000027108.
HOGENOM	HBG301263.
OMA	RGMGAKE.
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_STRP2

Accession

Primary (citable) accession number: Q04KR0

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	November 14, 2006
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