Pyridoxal-phosphate-dependent serine hydroxymethyltransferase - Heliobacterium modesticaldum (strain ATCC 51547 / Ice1)

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B0TI64 (GLYA_HELMI) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 32. 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:	Helmi_08590
ORF Names:	HM1_1090

Organism

Heliobacterium modesticaldum (strain ATCC 51547 / Ice1) [Complete proteome] [HAMAP]

Taxonomic identifier

Taxonomic lineage

Bacteria › Firmicutes › Clostridia › Clostridiales › Heliobacteriaceae › Heliobacterium

Protein attributes

Sequence length	413 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

413

Pyridoxal-phosphate-dependent serine hydroxymethyltransferase

PRO_0000369927

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

B0TI64 [UniParc].

Last modified April 8, 2008. Version 1.
Checksum: F62FFCC54730C1EE
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413

44,522

        10         20         30         40         50         60 
MSEWKHLHQV DPEVAAAMDR EKKRQKNNIE LIASENFVSE AVMEAAGSVL TNKYAEGYPG 

        70         80         90        100        110        120 
KRYYGGCEFV DQVERLAIER AKRLFGAEHA NVQPHSGANA NMGVYFACLE PGDTVLGMNL 

       130        140        150        160        170        180 
AHGGHLTHGS PVNISGKYFR FVAYGVDAHT GRIDYDEVAR IARETKPKLI VAGASAYPRV 

       190        200        210        220        230        240 
LDFARFRAIA DEVGAMLMVD MAHIAGLVAA GLHPSPVPYA EFVTTTTHKT LRGPRGGMIL 

       250        260        270        280        290        300 
CKQEWAAKVD KAIFPGLQGG PLMHIIAAKA VAFQEAMAPA FTAYQKQIAA NAAALAKGLT 

       310        320        330        340        350        360 
DRGFQLVSGG TDNHLMLVDL RNKQLTGKEA EKRLDECRIT VNKNAIPFDP QSPFVTSGIR 

       370        380        390        400        410 
IGTPAATSRG MDEAAMDQVA EAIHLCLSDG SEGAMQKAVA IVDALCARFP LYA

References

[1]

"The genome of Heliobacterium modesticaldum, a phototrophic representative of the Firmicutes containing the simplest photosynthetic apparatus."
Sattley W.M., Madigan M.T., Swingley W.D., Cheung P.C., Clocksin K.M., Conrad A.L., Dejesa L.C., Honchak B.M., Jung D.O., Karbach L.E., Kurdoglu A., Lahiri S., Mastrian S.D., Page L.E., Taylor H.L., Wang Z.T., Raymond J., Chen M., Blankenship R.E., Touchman J.W.
J. Bacteriol. 190:4687-4696(2008) [PubMed: 18441057] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 51547 / Ice1.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000930 Genomic DNA. Translation: ABZ83484.1.
RefSeq	YP_001679495.1. NC_010337.2.
3D structure databases
ProteinModelPortal	B0TI64.
SMR	B0TI64. Positions 5-405.
ModBase	Search...
Protein-protein interaction databases
STRING	B0TI64.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	5911383.
GenomeReviews	Gene locus Helmi_08590 in contig CP000930_GR.
KEGG	hmo:HM1_1090.
PATRIC	22105969. VBIHelMod36755_0786.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG301263.
OMA	DIAHTAG.
Enzyme and pathway databases
BioCyc	HMOD498761:HM1_1090-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_HELMI

Accession

Primary (citable) accession number: B0TI64

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 14, 2009
Last sequence update:	April 8, 2008
Last modified:	January 25, 2012
This is version 32 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