P0A825 (GLYA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

Gene names

Name:	glyA
Ordered Locus Names:	b2551, JW2535

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	417 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. Thus, is able to catalyze the cleavage of allothreonine and 3-phenylserine. Also catalyzes the irreversible conversion of 5,10-methenyltetrahydrofolate to 5-formyltetrahydrofolate. Ref.8
Catalytic activity	5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine. HAMAP-Rule MF_00051
Cofactor	Pyridoxal phosphate.
Pathway	One-carbon metabolism; tetrahydrofolate interconversion. HAMAP-Rule MF_00051 Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. HAMAP-Rule MF_00051
Subunit structure	Homodimer. Ref.15 Ref.18
Subcellular location	Cytoplasm HAMAP-Rule MF_00051.
Induction	By CsgD. Ref.12
Sequence similarities	Belongs to the SHMT family.
Biophysicochemical properties	Kinetic parameters: KM=7 µM for tetrahydrofolate (Ref.19) Ref.11 Ref.19 KM=140 µM for serine (Ref.19) KM=300 µM for serine (Ref.11)

Ontologies

Keywords
Biological process	Amino-acid biosynthesis One-carbon metabolism
Cellular component	Cytoplasm
Ligand	Pyridoxal phosphate
Molecular function	Transferase
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	L-serine catabolic process Inferred from direct assay PubMed 3891721. Source: EcoCyc glycine biosynthetic process from serine Inferred from direct assay PubMed 3891721. Source: EcoCyc glycine catabolic process Inferred from mutant phenotype PubMed 764875. Source: EcoCyc tetrahydrofolate interconversion Inferred from electronic annotation. Source: UniProtKB-UniPathway
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB membrane Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	glycine hydroxymethyltransferase activity Inferred from direct assay PubMed 3891721. Source: EcoCyc pyridoxal phosphate binding Inferred from direct assay Ref.13. Source: EcoCyc zinc ion binding Inferred from direct assay PubMed 11985624. Source: EcoliWiki
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		2	EBI-909080,EBI-909080

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 417

417

Serine hydroxymethyltransferase HAMAP-Rule MF_00051

PRO_0000113573

Regions

Region

125 – 127

3

Substrate binding HAMAP-Rule MF_00051

Region

355 – 357

3

Substrate binding HAMAP-Rule MF_00051

Sites

Binding site

35

1

Pyridoxal phosphate

Binding site

55

1

Pyridoxal phosphate

Binding site

57

1

Substrate

Binding site

64

1

Substrate

Binding site

65

1

Pyridoxal phosphate

Binding site

99

1

Pyridoxal phosphate

Binding site

121

1

Substrate; via carbonyl oxygen

Binding site

175

1

Pyridoxal phosphate

Binding site

203

1

Pyridoxal phosphate

Binding site

228

1

Pyridoxal phosphate

Binding site

235

1

Pyridoxal phosphate

Binding site

246

1

Substrate

Binding site

263

1

Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen

Binding site

363

1

Pyridoxal phosphate

Site

55

1

Transaldimination and stability

Site

235

1

Transaldimination and stability

Amino acid modifications

Modified residue

54

1

N6-acetyllysine Ref.14

Modified residue

62

1

N6-succinyllysine Ref.16

Modified residue

229

1

N6-(pyridoxal phosphate)lysine HAMAP-Rule MF_00051

Modified residue

242

1

N6-succinyllysine Ref.16

Modified residue

250

1

N6-acetyllysine; alternate Ref.14

Modified residue

250

1

N6-succinyllysine; alternate Ref.16

Modified residue

277

1

N6-succinyllysine Ref.16

Modified residue

285

1

N6-acetyllysine Ref.14

Modified residue

293

1

N6-succinyllysine Ref.16

Modified residue

331

1

N6-succinyllysine Ref.16

Modified residue

346

1

N6-succinyllysine Ref.16

Modified residue

354

1

N6-acetyllysine; alternate Ref.14

Modified residue

354

1

N6-succinyllysine; alternate Ref.16

Modified residue

375

1

N6-acetyllysine Ref.14

Experimental info

Mutagenesis

55

1

Y → F: 50 and 15-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 4-fold decrease in the catalytic efficiency. Ref.19

Mutagenesis

65

1

Y → F: Decrease in catalytic activity. Ref.17

Mutagenesis

85

1

L → A: Alteration of the dimer-monomer equilibrium accompanied by minor changes in the catalytic properties and whitout any significant change of tertiary structure. In the monomeric state; when associated with A-276. Ref.15

Mutagenesis

214

1

P → A: No significant difference in catalytic efficiency and affinity compared to the wild-type. Ref.11

Mutagenesis

214

1

P → G: No significant difference in catalytic efficiency and affinity compared to the wild-type. Ref.11

Mutagenesis

216

1

P → A: No significant difference in catalytic efficiency and affinity compared to the wild-type. Alteration in the folding rate. Ref.11

Mutagenesis

216

1

P → G: Important decrease in affinity and catalytic efficiency. Severely compromised in folding into a catalytically competent enzyme. Ref.11

Mutagenesis

218

1

P → A: No significant difference in catalytic efficiency and affinity compared to the wild-type. Ref.11

Mutagenesis

218

1

P → G: No significant difference in catalytic efficiency and affinity compared to the wild-type. Ref.11

Mutagenesis

235

1

R → K: 1500- and 20-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 15-fold decrease in the catalytic efficiency. Ref.19

Mutagenesis

235

1

R → L: 450- and 11-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 60-fold decrease in the catalytic efficiency. Ref.19

Mutagenesis

235

1

R → Q: 900- and 17-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 30-fold decrease in the catalytic efficiency. Ref.19

Mutagenesis

258

1

P → A: Important decrease in affinity and catalytic efficiency. Reduced thermal stability. Ref.11

Mutagenesis

258

1

P → G: Important decrease in affinity and catalytic efficiency. Ref.11

Mutagenesis

264

1

P → A: Important decrease in affinity and catalytic efficiency. Ref.11

Mutagenesis

264

1

P → G: Important decrease in affinity and catalytic efficiency. Ref.11

Mutagenesis

276

1

L → A: Alteration of the dimer-monomer equilibrium accompanied by minor changes in the catalytic properties and whitout any significant change of tertiary structure. In the monomeric state; when associated with A-85. Ref.15

Mutagenesis

363

1

R → A: It does not bind serine and glycine and shows no activity with serine as the substrate. Ref.9

Mutagenesis

363

1

R → K: Exhibits only 0.03% of the catalytic activity of the wild-type and a 15-fold reduction in affinity for glycine and serine. Ref.9

Mutagenesis

372

1

R → A: No significant difference compared to the wild-type. Ref.9

Mutagenesis

372

1

R → K: No significant difference compared to the wild-type. Ref.9

Secondary structure

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417

Helix Strand Turn

Details...

Helix

8 – 11

4

Helix

13 – 28

16

Beta strand

29 – 31

3

Helix

41 – 47

7

Helix

50 – 53

4

Beta strand

62 – 66

5

Helix

69 – 86

18

Beta strand

89 – 92

4

Helix

98 – 109

12

Beta strand

115 – 119

5

Turn

121 – 124

4

Helix

127 – 129

3

Helix

135 – 139

5

Beta strand

140 – 145

6

Beta strand

149 – 152

4

Helix

155 – 165

11

Beta strand

168 – 173

6

Helix

183 – 192

10

Beta strand

196 – 200

5

Turn

202 – 204

3

Helix

205 – 209

5

Turn

217 – 219

3

Beta strand

220 – 229

10

Beta strand

237 – 243

7

Helix

246 – 256

11

Turn

257 – 260

4

Helix

266 – 278

13

Helix

282 – 304

23

Helix

310 – 312

3

Beta strand

315 – 322

8

Helix

324 – 326

3

Helix

330 – 339

10

Turn

356 – 358

3

Beta strand

360 – 365

6

Helix

367 – 371

5

Helix

376 – 391

16

Turn

392 – 394

3

Helix

396 – 412

17

Beta strand

415 – 417

3

Sequences

	Sequence		Length	Mass (Da)
	P0A825 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 13E5558E99938539	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

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] [Europe PMC] [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. , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-7, FUNCTION AS A SERINE HYDROXYMETHYLTRANSFERASE.
[9]	"The function of arginine 363 as the substrate carboxyl-binding site in Escherichia coli serine hydroxymethyltransferase." Delle Fratte S., Iurescia S., Angelaccio S., Bossa F., Schirch V. Eur. J. Biochem. 225:395-401(1994) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ARG-363 AND ARG-372.
[10]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[11]	"Role of proline residues in the folding of serine hydroxymethyltransferase." Fu T.F., Boja E.S., Safo M.K., Schirch V. J. Biol. Chem. 278:31088-31094(2003) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF PRO-214; PRO-216; PRO-218; PRO-258 AND PRO-264, BIOPHYSICOCHEMICAL PROPERTIES.
[12]	"CsgD, a regulator of curli and cellulose synthesis, also regulates serine hydroxymethyltransferase synthesis in Escherichia coli K-12." Chirwa N.T., Herrington M.B. Microbiology 149:525-535(2003) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION.
[13]	"The mechanism of addition of pyridoxal 5'-phosphate to Escherichia coli apo-serine hydroxymethyltransferase." Malerba F., Bellelli A., Giorgi A., Bossa F., Contestabile R. Biochem. J. 404:477-485(2007) [PubMed] [Europe PMC] [Abstract] Cited for: REACTION MECHANISMN.
[14]	"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] [Europe PMC] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-54; LYS-250; LYS-285; LYS-354 AND LYS-375, MASS SPECTROMETRY. Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
[15]	"The role of evolutionarily conserved hydrophobic contacts in the quaternary structure stability of Escherichia coli serine hydroxymethyltransferase." Florio R., Chiaraluce R., Consalvi V., Paiardini A., Catacchio B., Bossa F., Contestabile R. FEBS J. 276:132-143(2009) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF LEU-85 AND LEU-276, SUBUNIT.
[16]	"Identification of lysine succinylation as a new post-translational modification." Zhang Z., Tan M., Xie Z., Dai L., Chen Y., Zhao Y. Nat. Chem. Biol. 7:58-63(2011) [PubMed] [Europe PMC] [Abstract] Cited for: SUCCINYLATION AT LYS-62; LYS-242; LYS-250; LYS-277; LYS-293; LYS-331; LYS-346 AND LYS-354. Strain: K12.
[17]	"Role of tyrosine 65 in the mechanism of serine hydroxymethyltransferase." Contestabile R., Angelaccio S., Bossa F., Wright H.T., Scarsdale N., Kazanina G., Schirch V. Biochemistry 39:7492-7500(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND PYRIDOXAL PHOSPHATE, MUTAGENESIS OF TYR-65.
[18]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, SUBUNIT.
[19]	"Role of a conserved active site cation-pi interaction in Escherichia coli serine hydroxymethyltransferase." Vivoli M., Angelucci F., Ilari A., Morea V., Angelaccio S., di Salvo M.L., Contestabile R. Biochemistry 48:12034-12046(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF MUTANT PHE-55 IN COMPLEX WITH PYRIDOXAL PHOSPHATE, MUTAGENESIS OF TYR-55 AND ARG-235, BIOPHYSICOCHEMICAL PROPERTIES.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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

NP_417046.1. NC_000913.2.
YP_490779.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]
3G8M	X-ray	3.30	A	1-417	[»]

ProteinModelPortal

P0A825.

SMR

P0A825. Positions 1-417.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36205N.

IntAct

P0A825. 7 interactions.

MINT

MINT-7293373.

STRING

511145.b2551.

2D gel databases

SWISS-2DPAGE

P0A825.

Proteomic databases

PaxDb

P0A825.

PRIDE

P0A825.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75604; AAC75604; b2551.
BAA16459; BAA16459; BAA16459.

GeneID

12932320.
947022.

KEGG

ecj:Y75_p2504.
eco:b2551.

PATRIC

32120501. VBIEscCol129921_2653.

Organism-specific databases

EchoBASE

EB0403.

EcoGene

EG10408. glyA.

Phylogenomic databases

eggNOG

COG0112.

HOGENOM

HOG000239404.

KO

K00600.

OMA

GKIDYED.

ProtClustDB

PRK00011.

Enzyme and pathway databases

BioCyc

EcoCyc:GLYOHMETRANS-MONOMER.
ECOL316407:JW2535-MONOMER.
MetaCyc:GLYOHMETRANS-MONOMER.

UniPathway

UPA00193.
UPA00288; UER01023.

Gene expression databases

Genevestigator

P0A825.

Family and domain databases

Gene3D

3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.

HAMAP

MF_00051. SHMT.

InterPro

IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
IPR001085. Ser_HO-MeTrfase.
IPR019798. Ser_HO-MeTrfase_PLP_BS.
[Graphical view]

PANTHER

PTHR11680. PTHR11680. 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...

Other

EvolutionaryTrace

P0A825.

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:	May 1, 2013
This is version 82 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program