Pyridoxal-phosphate-dependent serine hydroxymethyltransferase 1 - Vibrio vulnificus (strain YJ016)

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Q7MN19 (GLYA1_VIBVY) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 58. 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 1
Short name=SHMT 1
Short name=Serine methylase 1
EC=2.1.2.1

Gene names

Name:	glyA1
Ordered Locus Names:	VV0898

Organism

Vibrio vulnificus (strain YJ016) [Complete proteome] [HAMAP]

Taxonomic identifier

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio

Protein attributes

Sequence length	416 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

416

Pyridoxal-phosphate-dependent serine hydroxymethyltransferase 1

PRO_0000113696

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

Q7MN19 [UniParc].

Last modified December 15, 2003. Version 1.
Checksum: 5CE2AC55ACCC464E
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416

45,332

        10         20         30         40         50         60 
MLKRDMNIAD YDAELFAAIQ EETLRQEEHI ELIASENYTS PRVMEAQGSQ LTNKYAEGYP 

        70         80         90        100        110        120 
GKRYYGGCEY VDKAEALAID RACQLFGCEY ANVQPHSGSQ ANSAVYMALL NPGDTVLGMS 

       130        140        150        160        170        180 
LAHGGHLTHG SPVNFSGKHY NVIPYGIDEA GQINYDEMET LALEHKPKMI IGGFSAYSQI 

       190        200        210        220        230        240 
VDWKRMREIA DKVDAYLFVD MAHVAGLIAA GEYPTPVPHA HVVTTTTHKT LAGPRGGLIL 

       250        260        270        280        290        300 
SNAGEDMYKK LNSAVFPGGQ GGPLMHVIAG KAVAFKEAME PEFKAYQARV VKNAKAMVAQ 

       310        320        330        340        350        360 
FQERGYKIVS NGTENHLFLV DLIDKDITGK DADAALGAAN ITVNKNSVPN DPRSPFVTSG 

       370        380        390        400        410 
IRVGTPAITR RGFTEADAKE LANWMCDVLD NIGNEAVIEA TKQKVLEICK RLPVYA

References

[1]

"Comparative genome analysis of Vibrio vulnificus, a marine pathogen."
Chen C.-Y., Wu K.-M., Chang Y.-C., Chang C.-H., Tsai H.-C., Liao T.-L., Liu Y.-M., Chen H.-J., Shen A.B.-T., Li J.-C., Su T.-L., Shao C.-P., Lee C.-T., Hor L.-I., Tsai S.-F.
Genome Res. 13:2577-2587(2003) [PubMed: 14656965] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: YJ016.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000037 Genomic DNA. Translation: BAC93662.1.
RefSeq	NP_933691.1. NC_005139.1.
3D structure databases
ProteinModelPortal	Q7MN19.
SMR	Q7MN19. Positions 1-416.
ModBase	Search...
Protein-protein interaction databases
STRING	Q7MN19.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	2623676.
GenomeReviews	Gene locus VV0898 in contig BA000037_GR.
KEGG	vvy:VV0898.
PATRIC	20168580. VBIVibVul40472_0902.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0112.
HOGENOM	HBG301263.
OMA	KAICAKF.
PhylomeDB	Q7MN19.
ProtClustDB	PRK00011.
Enzyme and pathway databases
BioCyc	VVUL196600:VV0898-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

GLYA1_VIBVY

Accession

Primary (citable) accession number: Q7MN19

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 26, 2004
Last sequence update:	December 15, 2003
Last modified:	January 25, 2012
This is version 58 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