Pyridoxal-phosphate-dependent serine hydroxymethyltransferase - Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

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Q3IZN2 (GLYA_RHOS4) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 47. 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:	RHOS4_24340
ORF Names:	RSP_0823

Organism

Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

Taxonomic identifier

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhodobacterales › Rhodobacteraceae › Rhodobacter

Protein attributes

Sequence length	431 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 Reference 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

431

Pyridoxal-phosphate-dependent serine hydroxymethyltransferase

PRO_0000235014

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

Q3IZN2 [UniParc].

Last modified November 8, 2005. Version 1.
Checksum: 9BD0B30E66F97FC0
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431

45,734

        10         20         30         40         50         60 
MNAPHRDDGF FTESLSSRDP ELFASITGEL GRQRDEIELI ASENIVSRAV MEAQGSVMTN 

        70         80         90        100        110        120 
KYAEGYAGKR YYGGCDYVDV AETLAIERAK QLFGCAYVNV QPNSGSQANQ GVFQALIKPG 

       130        140        150        160        170        180 
DTILGMELAS GGHLTHGAAP NQSGKWFNAI QYGVRQQDQL IDYDQVAALA REHKPKLIIA 

       190        200        210        220        230        240 
GGSAIPRQID FARFRAIADE VGALLMVDMA HFAGLVAGGA HPSPFPHADV ATTTTHKTLR 

       250        260        270        280        290        300 
GPRGGMILTN SEEIAKKVNS AIFPGIQGGP LMHVIAAKAV AFGEALRPEF KAYAAQVVKN 

       310        320        330        340        350        360 
AQALADELMK GGLDIVTGGT DTHLMLVDLR PKGVKGNATE KALGRAHITC NKNGIPFDPE 

       370        380        390        400        410        420 
KPTVTSGVRL GTPAGTTRGF GEAEFREIGR LIVEVVDGLA ANGEEGNAAV EEAVKAKVAA 

       430 
LCARFPLYPT L

References

[1]

"Complete sequence of chromosome 1 of Rhodobacter sphaeroides 2.4.1."
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Richardson P., Mackenzie C., Choudhary M., Larimer F., Hauser L.J., Land M., Donohue T.J., Kaplan S.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000143 Genomic DNA. Translation: ABA80002.1.
RefSeq	YP_353903.1. NC_007493.1.
3D structure databases
ProteinModelPortal	Q3IZN2.
SMR	Q3IZN2. Positions 15-421.
ModBase	Search...
Protein-protein interaction databases
STRING	Q3IZN2.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	3718402.
GenomeReviews	Gene locus RHOS4_24340 in contig CP000143_GR.
KEGG	rsp:RSP_0823.
NMPDR	fig\|272943.3.peg.2455.
PATRIC	23154829. VBIRhoSph57909_2784.
Phylogenomic databases
eggNOG	COG0112.
HOGENOM	HBG301263.
OMA	IFNAGYA.
PhylomeDB	Q3IZN2.
ProtClustDB	PRK00011.
Enzyme and pathway databases
BioCyc	RSPH272943:RSP_0823-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_RHOS4

Accession

Primary (citable) accession number: Q3IZN2

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 16, 2006
Last sequence update:	November 8, 2005
Last modified:	January 25, 2012
This is version 47 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