Pyridoxal-phosphate-dependent serine hydroxymethyltransferase - Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / JCM 12257)

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B2RGR2 (GLYA_PORG3) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 29. 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:	PGN_0038

Organism

Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / JCM 12257) [Complete proteome] [HAMAP]

Taxonomic identifier

Taxonomic lineage

Bacteria › Bacteroidetes › Bacteroidia › Bacteroidales › Porphyromonadaceae › Porphyromonas

Protein attributes

Sequence length	426 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

426

Pyridoxal-phosphate-dependent serine hydroxymethyltransferase

PRO_1000091567

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

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

B2RGR2 [UniParc].

Last modified July 1, 2008. Version 1.
Checksum: C5F47D5C55BB853E
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426

46,674

        10         20         30         40         50         60 
MKKDSVIFDL IEKEHQRQLK GIELIASENF VSEQVMQAMG SCMTNKYAEG YPGKRYYGGC 

        70         80         90        100        110        120 
EVVDQSEQIA IDRIKQLYGA EWANVQPHSG AQANMAVLLA CLEAGDTFMG LNLEHGGHLS 

       130        140        150        160        170        180 
HGSLVNSSGI LYRPIGYNLS EETGMVDYDH MEKMAIEHKP KLIIGGGSAY SREWDYKRMR 

       190        200        210        220        230        240 
EIADKVGALL MIDMAHPAGL IAAGLLENPV KYAHIVTSTT HKTLRGPRGG IILMGKDFDN 

       250        260        270        280        290        300 
PWGKKTPKGE IKKMSALLDS AVFPGVQGGP LEHVIAAKAV AFGEALDPSF KEYQTQVKKN 

       310        320        330        340        350        360 
AAVLAQAFMD KGYKVISGGT DNHSMLIDLR PKFPELTGKV AEKALVAADI TVNKNMVPFD 

       370        380        390        400        410        420 
SRSAFQTSGF RVGTPAITTR GVKEDKMGYI VELIDRVLSA PEDEAVIASV RTEVNRMMAD 


YPLFAW

References

[1]

"Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis."
Naito M., Hirakawa H., Yamashita A., Ohara N., Shoji M., Yukitake H., Nakayama K., Toh H., Yoshimura F., Kuhara S., Hattori M., Hayashi T., Nakayama K.
DNA Res. 15:215-225(2008) [PubMed: 18524787] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 33277 / DSM 20709 / JCM 12257.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AP009380 Genomic DNA. Translation: BAG32557.1.
RefSeq	YP_001928154.1. NC_010729.1.
3D structure databases
ProteinModelPortal	B2RGR2.
SMR	B2RGR2. Positions 3-425.
ModBase	Search...
Protein-protein interaction databases
STRING	B2RGR2.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	6330474.
GenomeReviews	Gene locus PGN_0038 in contig AP009380_GR.
KEGG	pgn:PGN_0038.
PATRIC	22972985. VBIPorGin26334_0034.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG301263.
OMA	AHMTINK.
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_PORG3

Accession

Primary (citable) accession number: B2RGR2

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 24, 2009
Last sequence update:	July 1, 2008
Last modified:	January 25, 2012
This is version 29 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