Pyridoxal-phosphate-dependent serine hydroxymethyltransferase - Shewanella sediminis (strain HAW-EB3)

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A8FSQ9 (GLYA_SHESH) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 34. 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:	Ssed_1271

Organism

Shewanella sediminis (strain HAW-EB3) [Complete proteome] [HAMAP]

Taxonomic identifier

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Alteromonadales › Shewanellaceae › Shewanella

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_1000074910

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

A8FSQ9 [UniParc].

Last modified November 13, 2007. Version 1.
Checksum: 1B5180C2B523B598
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418

45,262

        10         20         30         40         50         60 
MLKKDMNIAD FDPQLFQAIA DETRRQEEHI ELIASENYTS PRVLEAQGSQ LTNKYAEGYP 

        70         80         90        100        110        120 
GKRYYGGCEH VDIAEELAIS RAKELFGATY ANVQPHSGSQ ANSAVFMALL QGGDTVLGMS 

       130        140        150        160        170        180 
LAHGGHLTHG SHVSFSGKLY NAVQYGIDEA TGKIDYAEVE RLAVEHKPKM IIAGFSAYSG 

       190        200        210        220        230        240 
IIDWGKFREI ADKVGAYLFV DMAHVAGLVA AGIYPNPLPH AHVVTTTTHK TLAGPRGGLI 

       250        260        270        280        290        300 
LSACDDEAIY KKLNSAVFPG GQGGPLMHVI AAKAVAFKEA LEPEFTAYQE QVVVNAKAMA 

       310        320        330        340        350        360 
KTFIERGYDV VSGGTDNHLF LLDLISKDIT GKDADAALGL ANITVNKNSV PNDPRSPFVT 

       370        380        390        400        410 
SGLRIGSPAI TRRGFKEEQS VELTNWMCDV LDDITDQGTI ERVKNQVLEL CARFPVYG

References

[1]

"Complete sequence of Shewanella sediminis HAW-EB3."
US DOE Joint Genome Institute
Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chertkov O., Brettin T., Bruce D., Detter J.C., Han C., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.

expand/collapse author list

Richardson P.
Submitted (AUG-2007) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: HAW-EB3.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000821 Genomic DNA. Translation: ABV35882.1.
RefSeq	YP_001473010.1. NC_009831.1.
3D structure databases
ProteinModelPortal	A8FSQ9.
SMR	A8FSQ9. Positions 1-418.
ModBase	Search...
Protein-protein interaction databases
STRING	A8FSQ9.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	5614044.
GenomeReviews	Gene locus Ssed_1271 in contig CP000821_GR.
KEGG	sse:Ssed_1271.
NMPDR	fig\|425104.3.peg.1114.
PATRIC	23559870. VBISheSed62411_1341.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0112.
HOGENOM	HBG301263.
OMA	GTSNHLM.
ProtClustDB	PRK00011.
Enzyme and pathway databases
BioCyc	SSED425104:SSED_1271-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_SHESH

Accession

Primary (citable) accession number: A8FSQ9

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 20, 2008
Last sequence update:	November 13, 2007
Last modified:	January 25, 2012
This is version 34 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