Serine hydroxymethyltransferase - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P0A825 (GLYA_ECOLI)

Last modified November 3, 2009. Version 48. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Serine hydroxymethyltransferase
      Short name=Serine methylase
      Short name=SHMT
    EC=2.1.2.1

Gene names

Name:	glyA
Ordered Locus Names:	b2551, JW2535

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	417 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Interconversion of serine and glycine. HAMAP MF_00051
Catalytic activity	5,10-methylenetetrahydrofolate + glycine + H₂O = tetrahydrofolate + L-serine. HAMAP MF_00051
Cofactor	Pyridoxal phosphate. HAMAP MF_00051
Pathway	One-carbon metabolism; tetrahydrofolate interconversion. HAMAP MF_00051
Subunit structure	Homotetramer. HAMAP MF_00051
Subcellular location	Cytoplasm. HAMAP MF_00051
Sequence similarities	Belongs to the SHMT family.

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Ontologies

Keywords
Biological process	One-carbon metabolism
Cellular component	Cytoplasm
Ligand	Pyridoxal phosphate
Molecular function	Transferase
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing
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: HAMAP
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB membrane Inferred from direct assay. Source: UniProtKB
Molecular function	glycine hydroxymethyltransferase activity Inferred from electronic annotation. Source: HAMAP pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 417

417

Serine hydroxymethyltransferase HAMAP MF_00051

PRO_0000113573

Amino acid modifications

Modified residue

N6-acetyllysine Ref.9

Modified residue

229

N6-(pyridoxal phosphate)lysine HAMAP MF_00051

Modified residue

250

N6-acetyllysine Ref.9

Modified residue

285

N6-acetyllysine Ref.9

Modified residue

354

N6-acetyllysine Ref.9

Modified residue

375

N6-acetyllysine Ref.9

Secondary structure

417

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P0A825-1 [UniParc].

Last modified July 21, 1986. Version 1.
Checksum: 13E5558E99938539
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FASTA

417

45,317

        10         20         30         40         50         60 
MLKREMNIAD YDAELWQAME QEKVRQEEHI ELIASENYTS PRVMQAQGSQ LTNKYAEGYP 

        70         80         90        100        110        120 
GKRYYGGCEY VDIVEQLAID RAKELFGADY ANVQPHSGSQ ANFAVYTALL EPGDTVLGMN 

       130        140        150        160        170        180 
LAHGGHLTHG SPVNFSGKLY NIVPYGIDAT GHIDYADLEK QAKEHKPKMI IGGFSAYSGV 

       190        200        210        220        230        240 
VDWAKMREIA DSIGAYLFVD MAHVAGLVAA GVYPNPVPHA HVVTTTTHKT LAGPRGGLIL 

       250        260        270        280        290        300 
AKGGSEELYK KLNSAVFPGG QGGPLMHVIA GKAVALKEAM EPEFKTYQQQ VAKNAKAMVE 

       310        320        330        340        350        360 
VFLERGYKVV SGGTDNHLFL VDLVDKNLTG KEADAALGRA NITVNKNSVP NDPKSPFVTS 

       370        380        390        400        410 
GIRVGTPAIT RRGFKEAEAK ELAGWMCDVL DSINDEAVIE RIKGKVLDIC ARYPVYA

« Hide

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete nucleotide sequence of the E. coli glyA gene." Plamann M.D., Stauffer L.T., Urbanowski M.L., Stauffer G.V. Nucleic Acids Res. 11:2065-2075(1983) [PubMed: 6300791] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. Horiuchi T. DNA Res. 4:91-113(1997) [PubMed: 9205837] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed: 9298646] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-19. Strain: K12 / EMG2.
[6]	"Isolation and nucleotide sequence of the hmp gene that encodes a haemoglobin-like protein in Escherichia coli K-12." Vasudevan S.G., Armarego W.L.F., Shaw D.C., Lilley P.E., Dixon N.E., Poole R.K. Mol. Gen. Genet. 226:49-58(1991) [PubMed: 2034230] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-17. Strain: K12.
[7]	Pasquali C., Sanchez J.-C., Ravier F., Golaz O., Hughes G.J., Frutiger S., Paquet N., Wilkins M., Appel R.D., Bairoch A., Hochstrasser D.F. Submitted (SEP-1994) to UniProtKB Cited for: PROTEIN SEQUENCE OF 1-11. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]	"Characterization of the Escherichia coli gene for serine hydroxymethyltransferase." Plamann M.D., Stauffer G.V. Gene 22:9-18(1983) [PubMed: 6190704] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-7.
[9]	"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y. Mol. Cell. Proteomics 8:215-225(2009) [PubMed: 18723842] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-54; LYS-250; LYS-285; LYS-354 AND LYS-375, MASS SPECTROMETRY.
[10]	"Crystal structure at 2.4-A resolution of E. coli serine hydroxymethyltransferase in complex with glycine substrate and 5-formyl tetrahydrofolate." Scarsdale J.N., Radaev S., Kazanina G., Schirch V., Wright H.T. J. Mol. Biol. 296:155-168(2000) [PubMed: 10656824] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
+	Additional computationally mapped references.

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Cross-references

Sequence databases

V00283 Genomic DNA. Translation: CAA23547.1.
U00096 Genomic DNA. Translation: AAC75604.1.
AP009048 Genomic DNA. Translation: BAA16459.1.
J01620 Genomic DNA. Translation: AAA23912.1.

PIR

XYECS. A00559.

RefSeq

AP_003137.1.
NP_417046.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DFO	X-ray	2.40	A/B/C/D	1-417	[»]
1EQB	X-ray	2.70	A/B/C/D	1-417	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

P0A825.

2-D gel databases

SWISS-2DPAGE

P0A825.

2DBase-Ecoli

P0A825.

ECO2DBASE

G043.8. 6TH EDITION.

Genome annotation databases

GeneID

947022.

GenomeReviews

Gene locus JW2535 in contig AP009048_GR.
Gene locus b2551 in contig U00096_GR.

KEGG

ecj:JW2535.
eco:b2551.

Organism-specific databases

EchoBASE

EB0403.

EcoGene

EG10408. glyA.

CMR

Search...

Phylogenomic databases

HOGENOM

P0A825.

OMA

YNFVSYS.

Enzyme and pathway databases

BioCyc

EcoCyc:GLYOHMETRANS-MON.
MetaCyc:GLYOHMETRANS-MON.

Gene expression databases

Genevestigator

P0A825.

Family and domain databases

HAMAP

MF_00051.
[Tree]

InterPro

IPR015421. PyrdxlP-dep_Trfase_major_sub1.
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.

PANTHER

PTHR11680. Gly_HO-Metrfase. 1 hit.

Pfam

PF00464. SHMT. 1 hit.
[Graphical view]

PIRSF

PIRSF000412. SHMT. 1 hit.

PROSITE

PS00096. SHMT. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

GLYA_ECOLI

Accession

Primary (citable) accession number: P0A825
Secondary accession number(s): P00477

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	November 3, 2009
This is version 48 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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