EzCatDB D00085

glycine hydroxymethyltransferase
serine aldolase
threonine aldolase
serine hydroxymethylase
serine hydroxymethyltransferase
allothreonine aldolase
L-serine hydroxymethyltransferase
L-threonine aldolase
serine hydroxymethyltransferase
serine transhydroxymethylase

Synonyms

SHMT
Serine methylase
EC 2.1.2.1

SHMT
EC 2.1.2.1
Glycine hydroxymethyltransferase
Serine methylase

RefSeq

NP_417046.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490779.1 (Protein)
NC_007779.1 (DNA/RNA sequence)

YP_144790.1 (Protein)
NC_006461.1 (DNA/RNA sequence)

NP_033197.2 (Protein)
NM_009171.2 (DNA/RNA sequence)

NP_001095187.1 (Protein)
NM_001101717.1 (DNA/RNA sequence)

NP_004160.3 (Protein)
NM_004169.3 (DNA/RNA sequence)
NP_683718.1 (Protein)
NM_148918.1 (DNA/RNA sequence)

NP_001159828.1 (Protein)
NM_001166356.1 (DNA/RNA sequence)
NP_001159829.1 (Protein)
NM_001166357.1 (DNA/RNA sequence)
NP_001159830.1 (Protein)
NM_001166358.1 (DNA/RNA sequence)
NP_001159831.1 (Protein)
NM_001166359.1 (DNA/RNA sequence)
NP_005403.2 (Protein)
NM_005412.5 (DNA/RNA sequence)

Pfam

PF00464 (SHMT)
[Graphical view]

KEGG pathways

MAP code

Pathways

MAP00260

Glycine, serine and threonine metabolism

MAP00460

Cyanoamino acid metabolism

MAP00670

One carbon pool by folate

MAP00680

Methane metabolism

UniProtKB:Accession Number

Entry name

GLYA_ECOLI

GLYA_THET8

Q7SIB6_BACST

GLYC_MOUSE

GLYC_RABIT

GLYC_HUMAN

GLYM_HUMAN

Activity

5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine.

Subunit

Homotetramer.

Homotetramer (By similarity).

Homotetramer.

Subcellular location

Cytoplasm.

Cytoplasm (By similarity).

Cytoplasm.

Mitochondrion.

Cofactor

Pyridoxal phosphate.

Pyridoxal phosphate (By similarity).

Pyridoxal phosphate.,Pyridoxal phosphate (By similarity).

Pyridoxal phosphate (By similarity).

Pyridoxal phosphate.

Compound table: links to PDB-related databases & PoSSuM

Cofactors

Substrates

Products

intermediates

KEGG-id

Compound

Pyridoxal phosphate

L-Serine

Tetrahydrofolate

Glycine

5,10-Methylenetetrahydrofolate

H2O

External aldimine intermediate (PLP-L-Ser)

Formaldehyde

Quinonoid intermediate (PLP-Gly)

5-hydroxymethylene-tetrahydrofolate

5-iminium-tetrahydrofolate

External aldimine intermediate (PLP-Gly)

Gem-diamine transition-state (active-site-Lys-PLP-Gly)

Type

aromatic ring (with nitrogen atoms),phosphate group/phosphate ion

amino acids,carbohydrate

amino acids,amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl group

amino acids

amino acids,amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl group

H2O

ChEBI

PubChem

Analogue:PLG

Unbound

Intermediate-analogue:FFO

Intermediate-bound:PLG

Unbound

1dfoB01

Analogue:PLG

Unbound

Intermediate-analogue:FFO

Intermediate-bound:PLG

Unbound

1dfoC01

Analogue:PLG

Unbound

Intermediate-analogue:FFO

Intermediate-bound:PLG

Unbound

1dfoD01

Analogue:PLG

Unbound

Intermediate-analogue:FFO

Intermediate-bound:PLG

Unbound

1eqbA01

Bound:PLP

Unbound

Intermediate-analogue:FFO

Intermediate-bound:GLY-PLP

Unbound

1eqbB01

Bound:PLP

Unbound

Intermediate-analogue:FFO

Intermediate-bound:GLY-PLP

Unbound

1eqbC01

Bound:PLP

Unbound

Intermediate-analogue:FFO

Intermediate-bound:GLY-PLP

Unbound

1eqbD01

Bound:PLP

Unbound

Intermediate-analogue:FFO

Intermediate-bound:GLY-PLP

Unbound

2dkjA01

Bound:PLP

Unbound

2dkjB01

Bound:PLP

Unbound

1kkjA02

Bound:PLP

Unbound

1kkpA02

Bound:PLP

Unbound

Intermediate-bound:SER-PLP

Unbound

1kl1A02

Bound:PLP

Unbound

Intermediate-bound:GLY-PLP

Unbound

1kl2A02

Bound:PLP

Unbound

Intermediate-analogue:FON

Intermediate-bound:GLY-PLP

Unbound

1kl2B02

Bound:PLP

Unbound

Intermediate-analogue:FON

Intermediate-bound:GLY-PLP

Unbound

1yjsA02

Bound:PLP

Unbound

Intermediate-bound:GLY-PLP

Unbound

1yjyA02

Bound:PLP

Unbound

Intermediate-bound:SER-PLP

Unbound

1yjzA02

Bound:PLP

Unbound

2vgtA01

Bound:PLP

Unbound

Intermediate-bound:GLY-PLP

Unbound

2vguA01

Bound:PLP

Unbound

Intermediate-bound:SER-PLP

Unbound

2vgvA01

Bound:PLP

Unbound

Intermediate-bound:GLY-PLP

Unbound

2vgwA01

Bound:PLP

Unbound

Transition-state-bound:GLY-PLP-LYS 226

2vi9A01

Bound:PLP

Unbound

Intermediate-bound:GLY-PLP

Unbound

2viaA01

Bound:PLP

Unbound

Intermediate-bound:SER-PLP

Unbound

2vibA01

Bound:PLP

Unbound

Intermediate-bound:GLY-PLP

Unbound

1ejiA02

Analogue:PLG

Unbound

Intermediate-bound:PLG

Intermediate-bound:THF

Unbound

1ejiB02

Analogue:PLG

Unbound

Intermediate-bound:PLG

Intermediate-bound:THF

Unbound

1ejiC02

Analogue:PLG

Unbound

Transition-state-bound:PLG-LYS 257

1ejiD02

Analogue:PLG

Unbound

Intermediate-bound:THF

Unbound

Transition-state-bound:PLG-LYS 257

1cj0A02

Bound:PLP

Unbound

1cj0B02

Bound:PLP

Unbound

1ls3A02

Bound:PLP

Unbound

Transition-state-bound:GLY-PLP-LYS 229

1ls3B02

Bound:PLP

Unbound

Intermediate-analogue:TGF

Unbound

1ls3C02

Bound:PLP

Unbound

Transition-state-bound:GLY-PLP-LYS 229

1ls3D02

Bound:PLP

Unbound

Intermediate-analogue:TGF

Unbound

1rv3A02

Bound:PLP

Unbound

1rv3B02

Bound:PLP

Unbound

Transition-state-bound:GLY-PLP-LYS 257

1rv4A02

Bound:PLP

Unbound

1rv4B02

Bound:PLP

Unbound

1rvuA02

Bound:PLP

Unbound

1rvuB02

Bound:PLP

Unbound

1rvyA02

Bound:PLP

Unbound

Transition-state-bound:PLG-LYS 257

1rvyB02

Bound:PLP

Unbound

1bj4A01

Bound:PLP

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Unbound

Active-site residues

resource

literature[26], [30], [31], [38], [41], [46], [48]

pdb

Catalytic residues

Cofactor-binding residues

comment

1dfoA01

GLU 57;TYR 65;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

1dfoB01

GLU 57;TYR 65;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

1dfoC01

GLU 57;TYR 65;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

1dfoD01

GLU 57;TYR 65;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

1eqbA01

GLU 57; ;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

mutant Y65F

1eqbB01

GLU 57; ;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

mutant Y65F

1eqbC01

GLU 57; ;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

mutant Y65F

1eqbD01

GLU 57; ;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

mutant Y65F

2dkjA01

GLU 53;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

2dkjB01

GLU 53;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

1kkjA02

GLU 53;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

1kkpA02

GLU 53;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

1kl1A02

GLU 53;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

1kl2A02

GLU 53;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

1kl2B02

GLU 53;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

1yjsA02

GLU 53;TYR 61;ASP 197;THR 223;

mutant K226Q

1yjyA02

GLU 53;TYR 61;ASP 197;THR 223;

mutant K226M

1yjzA02

GLU 53;TYR 61;ASP 197;THR 223;

mutant K226M

2vgtA01

;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

mutant E53Q

2vguA01

;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

mutant E53Q

2vgvA01

;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

mutant E53Q

2vgwA01

;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

mutant E53Q

2vi9A01

GLU 53;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

mutant S172A

2viaA01

GLU 53;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

mutant S172A

2vibA01

GLU 53;TYR 61;ASP 197;THR 223;LYS 226

LYS 226(Pyridoxal phosphate binding)

mutant S172A

1ejiA02

GLU 75;TYR 83;ASP 228;THR 254;LYS 257

LYS 257(Pyridoxal phosphate binding)

1ejiB02

GLU 75;TYR 83;ASP 228;THR 254;LYS 257

LYS 257(Pyridoxal phosphate binding)

1ejiC02

GLU 75;TYR 83;ASP 228;THR 254;LYS 257

LYS 257(Pyridoxal phosphate binding)

1ejiD02

GLU 75;TYR 83;ASP 228;THR 254;LYS 257

LYS 257(Pyridoxal phosphate binding)

1cj0A02

GLU 57;TYR 65;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

1cj0B02

GLU 57;TYR 65;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

1ls3A02

GLU 57;TYR 65;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

1ls3B02

GLU 57;TYR 65;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

1ls3C02

GLU 57;TYR 65;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

1ls3D02

GLU 57;TYR 65;ASP 200;THR 226;LYS 229

LYS 229(Pyridoxal phosphate binding)

1rv3A02

;TYR 83;ASP 228;THR 254;LYS 257

LYS 257(Pyridoxal phosphate binding)

mutant E75L

1rv3B02

;TYR 83;ASP 228;THR 254;LYS 257

LYS 257(Pyridoxal phosphate binding)

mutant E75L

1rv4A02

;TYR 83;ASP 228;THR 254;LYS 257

LYS 257(Pyridoxal phosphate binding)

mutant E75L

1rv4B02

;TYR 83;ASP 228;THR 254;LYS 257

LYS 257(Pyridoxal phosphate binding)

mutant E75L

1rvuA02

;TYR 83;ASP 228;THR 254;LYS 257

LYS 257(Pyridoxal phosphate binding)

mutant E75Q

1rvuB02

;TYR 83;ASP 228;THR 254;LYS 257

LYS 257(Pyridoxal phosphate binding)

mutant E75Q

1rvyA02

;TYR 83;ASP 228;THR 254;LYS 257

LYS 257(Pyridoxal phosphate binding)

mutant E75Q

1rvyB02

;TYR 83;ASP 228;THR 254;LYS 257

LYS 257(Pyridoxal phosphate binding)

mutant E75Q

1bj4A01

GLU 75;TYR 83;ASP 228;THR 254;LYS 257

LYS 257(Pyridoxal phosphate binding)

2a7vA01

GLU 82; ;ASP 235;THR 261;LYS 264

LYS 264(Pyridoxal phosphate binding)

invisible 84-95, 148-178

References for Catalytic Mechanism

References

Sections

No. of steps in catalysis

[17]

Fig.6, p.24360-24361

[22]

Figure 1, p.1105, p.1110-1113

[25]

Scheme 1, p.8352-8357

[26]

Fig.17, Fig.18, p.394-397

[28]

Scheme 1, p.7499

[29]

Fig.1, p.13320-13223

[30]

Scheme 1, p.5974-5975

[31]

Fig.4, p.1443-1446

[33]

p.411-413

[34]

Scheme 1, p.156-157, p.162-166

[36]

Scheme 1

[38]

Scheme I, Scheme II, p.17168

[41]

Fig.1, p.24-25, p.27-28

[47]

Fig.1, p.6865-6867

[49]

Scheme 1, p.6930, p.6935-6936

[50]

p.4154-4155

references

[1]

PubMed ID

3536510

Journal

Eur J Biochem

Year

1986

Volume

161

Pages

45-9

Authors

Schirch V, Schirch D, Martini F, Bossa F

Title

Serine hydroxymethyltransferase. Effect of proteases on the activity and structure of the cytosolic enzyme.

[2]

PubMed ID

1849406

Journal

Biochem J

Year

1991

Volume

274

Pages

807-12

Authors

Malthouse JP, Milne JJ, Gariani LS

Title

A comparative study of the kinetics and stereochemistry of the serine hydroxymethyltransferase- and tryptophan synthase-catalysed exchange of the pro-2R and pro-2S protons of glycine.

[3]

PubMed ID

1765122

Journal

Experientia

Year

1991

Volume

Pages

1104-18

Authors

Smith DM, Thomas NR, Gani D

Title

A comparison of pyridoxal 5'-phosphate dependent decarboxylase and transaminase enzymes at a molecular level.

[4]

PubMed ID

1536856

Journal

Biochemistry

Year

1992

Volume

Pages

2155-64

Authors

Stover P, Schirch V

Title

Enzymatic mechanism for the hydrolysis of 5,10-methenyltetrahydropteroylglutamate to 5-formyltetrahydropteroylglutamate by serine hydroxymethyltransferase.

[5]

PubMed ID

1577761

Journal

J Biol Chem

Year

1992

Volume

267

Pages

9289-93

Authors

Usha R, Savithri HS, Rao NA

Title

Arginine residues involved in binding of tetrahydrofolate to sheep liver serine hydroxymethyltransferase.

[6]

PubMed ID

8405393

Journal

FEBS Lett

Year

1993

Volume

331

Pages

145-9

Authors

Pascarella S, Schirch V, Bossa F

Title

Similarity between serine hydroxymethyltransferase and other pyridoxal phosphate-dependent enzymes.

[7]

PubMed ID

8226831

Journal

J Biol Chem

Year

1993

Volume

268

Pages

23132-8

Authors

Schirch D, Delle Fratte S, Iurescia S, Angelaccio S, Contestabile R, Bossa F, Schirch V

Title

Function of the active-site lysine in Escherichia coli serine hydroxymethyltransferase.

[8]

PubMed ID

8478924

Journal

J Mol Biol

Year

1993

Volume

230

Pages

1094-6

Authors

Stover P, Kruschwitz H, Schirch V, Wright HT

Title

Diffraction grade crystals of Escherichia coli serine hydroxymethyltransferase.

[9]

PubMed ID

7947980

Journal

Biochim Biophys Acta

Year

1994

Volume

1209

Pages

40-50

Authors

Bhaskar B, Prakash V, Savithri HS, Rao NA

Title

Interactions of L-serine at the active site of serine hydroxymethyltransferases: induction of thermal stability.

[10]

PubMed ID

8003988

Journal

Protein Sci

Year

1994

Volume

Pages

701-5

Authors

Pascarella S, Bossa F

Title

Similarity between pyridoxal/pyridoxamine phosphate-dependent enzymes involved in dideoxy and deoxyaminosugar biosynthesis and other pyridoxal phosphate enzymes.

[11]

PubMed ID

8674620

Journal

Biochem Soc Trans

Year

1996

Volume

Pages

132S

Authors

Fitzpatrick TB, Malthouse JP

Title

Proof that serine hydroxymethyltransferase retains its specificity for the pro-2S proton of glycine in the absence of tetrahydrofolate.

[12]

PubMed ID

8910307

Journal

J Biol Chem

Year

1996

Volume

271

Pages

27311-20

Authors

Cai K, Schirch V

Title

Structural studies on folding intermediates of serine hydroxymethyltransferase using fluorescence resonance energy transfer.

[13]

PubMed ID

8621691

Journal

J Biol Chem

Year

1996

Volume

271

Pages

2987-94

Authors

Cai K, Schirch V

Title

Structural studies on folding intermediates of serine hydroxymethyltransferase using single tryptophan mutants.

[14]

PubMed ID

8860659

Journal

Protein Expr Purif

Year

1996

Volume

Pages

323-8

Authors

Iurescia S, Condo I, Angelaccio S, Delle Fratte S, Bossa F

Title

Site-directed mutagenesis techniques in the study of Escherichia coli serine hydroxymethyltransferase.

[15]

PubMed ID

9584848

Journal

Acta Biochim Pol

Year

1997

Volume

Pages

679-88

Authors

Talwar R, Jagath JR, Datta A, Prakash V, Savithri HS, Rao NA

Title

The role of lysine-256 in the structure and function of sheep liver recombinant serine hydroxymethyltransferase.

[16]

PubMed ID

9398220

Journal

Biochemistry

Year

1997

Volume

Pages

14956-64

Authors

Kastanos EK, Woldman YY, Appling DR

Title

Role of mitochondrial and cytoplasmic serine hydroxymethyltransferase isozymes in de novo purine synthesis in Saccharomyces cerevisiae.

[17]

PubMed ID

9305893

Journal

J Biol Chem

Year

1997

Volume

272

Pages

24355-62

Authors

Jagath JR, Sharma B, Rao NA, Savithri HS

Title

The role of His-134, -147, and -150 residues in subunit assembly, cofactor binding, and catalysis of sheep liver cytosolic serine hydroxymethyltransferase.

[18]

Comments

X-ray crystallography

PubMed ID

9757129

Journal

Acta Crystallogr D Biol Crystallogr

Year

1998

Volume

Pages

1030-1

Authors

Renwick SB, Skelly JV, Chave KJ, Sanders PG, Snell K, Baumann U

Title

Purification, crystallization and preliminary X-ray analysis of human recombinant cytosolic serine hydroxymethyltransferase.

Related PDB

1bj4

[19]

PubMed ID

9523719

Journal

Eur J Biochem

Year

1998

Volume

252

Pages

113-7

Authors

Fitzpatrick TB, Malthouse JP

Title

A substrate-induced change in the stereospecificity of the serine-hydroxymethyltransferase-catalysed exchange of the alpha-protons of amino acids--evidence for a second catalytic site.

[20]

PubMed ID

9843671

Journal

J Struct Biol

Year

1998

Volume

123

Pages

169-74

Authors

Kazanina G, Radaev S, Wright HT, Schirch V

Title

Crystal forms and subunit stoichiometry of serine hydroxymethyltransferase.

[21]

PubMed ID

9761478

Journal

Protein Sci

Year

1998

Volume

Pages

1976-82

Authors

Pascarella S, Angelaccio S, Contestabile R, Delle Fratte S, Di Salvo M, Bossa F

Title

The structure of serine hydroxymethyltransferase as modeled by homology and validated by site-directed mutagenesis.

[22]

Comments

X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS) OF 11-480

Medline ID

98428667

PubMed ID

9753690

Journal

Structure

Year

1998

Volume

Pages

1105-16

Authors

Renwick SB, Snell K, Baumann U

Title

The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy.

Related UniProtKB

P34896

[23]

PubMed ID

10600164

Journal

Arch Biochem Biophys

Year

1999

Volume

372

Pages

271-9

Authors

di Salvo ML, Delle Fratte S, Maras B, Bossa F, Wright HT, Schirch V

Title

Deamidation of asparagine residues in a recombinant serine hydroxymethyltransferase.

[24]

PubMed ID

10493937

Journal

Biochem J

Year

1999

Volume

343 Pt 1

Pages

257-63

Authors

Krishna Rao JV, Jagath JR, Sharma B, Appaji Rao N, Savithri HS

Title

Asp-89: a critical residue in maintaining the oligomeric structure of sheep liver cytosolic serine hydroxymethyltransferase.

[25]

PubMed ID

10387080

Journal

Biochemistry

Year

1999

Volume

Pages

8347-58

Authors

Scarsdale JN, Kazanina G, Radaev S, Schirch V, Wright HT

Title

Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8 A resolution: mechanistic implications.

Related PDB

1cj0

[26]

PubMed ID

10828359

Journal

Adv Enzyme Regul

Year

2000

Volume

Pages

353-403

Authors

Snell K, Baumann U, Byrne PC, Chave KJ, Renwick SB, Sanders PG, Whitehouse SK

Title

The genetic organization and protein crystallographic structure of human serine hydroxymethyltransferase.

[27]

PubMed ID

10970801

Journal

Biochem J

Year

2000

Volume

350 Pt 3

Pages

849-53

Authors

Talwar R, Leelavathy V, Krishna Rao JV, Appaji Rao N, Savithri HS

Title

Role of pro-297 in the catalytic mechanism of sheep liver serine hydroxymethyltransferase.

[28]

Comments

X-ray crystallography

PubMed ID

10858298

Journal

Biochemistry

Year

2000

Volume

Pages

7492-500

Authors

Contestabile R, Angelaccio S, Bossa F, Wright HT, Scarsdale N, Kazanina G, Schirch V

Title

Role of tyrosine 65 in the mechanism of serine hydroxymethyltransferase.

Related PDB

1eqb

[29]

Comments

X-ray crystallography

PubMed ID

11063567

Journal

Biochemistry

Year

2000

Volume

Pages

13313-23

Authors

Szebenyi DM, Liu X, Kriksunov IA, Stover PJ, Thiel DJ

Title

Structure of a murine cytoplasmic serine hydroxymethyltransferase quinonoid ternary complex: evidence for asymmetric obligate dimers.

Related PDB

1eji

[30]

PubMed ID

10998057

Journal

Eur J Biochem

Year

2000

Volume

267

Pages

5967-76

Authors

Rao JV, Prakash V, Rao NA, Savithri HS

Title

The role of Glu74 and Tyr82 in the reaction catalyzed by sheep liver cytosolic serine hydroxymethyltransferase.

[31]

PubMed ID

10691982

Journal

Eur J Biochem

Year

2000

Volume

267

Pages

1441-6

Authors

Talwar R, Jagath JR, Rao NA, Savithri HS

Title

His230 of serine hydroxymethyltransferase facilitates the proton abstraction step in catalysis.

[32]

PubMed ID

10716626

Journal

Int J Biochem Cell Biol

Year

2000

Volume

Pages

289-301

Authors

Ogawa H, Gomi T, Fujioka M

Title

Serine hydroxymethyltransferase and threonine aldolase: are they identical?

[33]

PubMed ID

10762066

Journal

Int J Biochem Cell Biol

Year

2000

Volume

Pages

405-16

Authors

Rao NA, Talwar R, Savithri HS

Title

Molecular organization, catalytic mechanism and function of serine hydroxymethyltransferase--a potential target for cancer chemotherapy.

[34]

Comments

X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS)

Medline ID

20124005

PubMed ID

10656824

Journal

J Mol Biol

Year

2000

Volume

296

Pages

155-68

Authors

Scarsdale JN, Radaev S, Kazanina G, Schirch V, Wright HT

Title

Crystal structure at 2.4 A resolution of E. coli serine hydroxymethyltransferase in complex with glycine substrate and 5-formyl tetrahydrofolate.

Related PDB

Related UniProtKB

PubMed ID

Journal

Biochemistry

Year

2001

Volume

Pages

4932-9

Authors

Liu X, Szebenyi DM, Anguera MC, Thiel DJ, Stover PJ

Title

Lack of catalytic activity of a murine mRNA cytoplasmic serine hydroxymethyltransferase splice variant: evidence against alternative splicing as a regulatory mechanism.

[36]

PubMed ID

11737206

Journal

Eur J Biochem

Year

2001

Volume

268

Pages

6508-25

Authors

Contestabile R, Paiardini A, Pascarella S, di Salvo ML, D'Aguanno S, Bossa F

Title

l-Threonine aldolase, serine hydroxymethyltransferase and fungal alanine racemase. A subgroup of strictly related enzymes specialized for different functions.

[37]

PubMed ID

12356312

Journal

Biochemistry

Year

2002

Volume

Pages

12115-23

Authors

Bhatt AN, Prakash K, Subramanya HS, Bhakuni V

Title

Different unfolding pathways for mesophilic and thermophilic homologues of serine hydroxymethyltransferase.

[38]

PubMed ID

11877399

Journal

J Biol Chem

Year

2002

Volume

277

Pages

17161-9

Authors

Trivedi V, Gupta A, Jala VR, Saravanan P, Rao GS, Rao NA, Savithri HS, Subramanya HS

Title

Crystal structure of binary and ternary complexes of serine hydroxymethyltransferase from Bacillus stearothermophilus: insights into the catalytic mechanism.

Related PDB

1kkj,1kkp,1kl1,1kl2

[39]

PubMed ID

12089472

Journal

J Biosci

Year

2002

Volume

Pages

233-42

Authors

Jala VR, Prakash V, Rao NA, Savithri HS

Title

Overexpression and characterization of dimeric and tetrameric forms of recombinant serine hydroxymethyltransferase from Bacillus stearothermophilus.

[40]

PubMed ID

12392447

Journal

Biochem J

Year

2003

Volume

369

Pages

469-76

Authors

Jala VR, Appaji Rao N, Savithri HS

Title

Identification of amino acid residues, essential for maintaining the tetrameric structure of sheep liver cytosolic serine hydroxymethyltransferase, by targeted mutagenesis.

[41]

PubMed ID

12686103

Journal

Biochim Biophys Acta

Year

2003

Volume

1647

Pages

24-9

Authors

Appaji Rao N, Ambili M, Jala VR, Subramanya HS, Savithri HS

Title

Structure-function relationship in serine hydroxymethyltransferase.

[42]

PubMed ID

12686123

Journal

Biochim Biophys Acta

Year

2003

Volume

1647

Pages

138-42

Authors

Malthouse JP

Title

Stereospecificity of alpha-proton exchange reactions catalysed by pyridoxal-5'-phosphate-dependent enzymes.

[43]

PubMed ID

12902326

Journal

J Biol Chem

Year

2003

Volume

278

Pages

41789-97

Authors

Angelaccio S, Chiaraluce R, Consalvi V, Buchenau B, Giangiacomo L, Bossa F, Contestabile R

Title

Catalytic and thermodynamic properties of tetrahydromethanopterin-dependent serine hydroxymethyltransferase from Methanococcus jannaschii.

[44]

PubMed ID

12773539

Journal

J Biol Chem

Year

2003

Volume

278

Pages

31088-94

Authors

Fu TF, Boja ES, Safo MK, Schirch V

Title

Role of proline residues in the folding of serine hydroxymethyltransferase.

[45]

PubMed ID

12514178

Journal

J Biol Chem

Year

2003

Volume

278

Pages

10142-9

Authors

Zanetti KA, Stover PJ

Title

Pyridoxal phosphate inhibits dynamic subunit interchange among serine hydroxymethyltransferase tetramers.

[46]

PubMed ID

12438316

Journal

J Biol Chem

Year

2003

Volume

278

Pages

2645-53

Authors

Fu TF, Scarsdale JN, Kazanina G, Schirch V, Wright HT

Title

Location of the pteroylpolyglutamate-binding site on rabbit cytosolic serine hydroxymethyltransferase.

Related PDB

1ls3

[47]

PubMed ID

15170323

Journal

Biochemistry

Year

2004

Volume

Pages

6865-76

Authors

Szebenyi DM, Musayev FN, di Salvo ML, Safo MK, Schirch V

Title

Serine hydroxymethyltransferase: role of glu75 and evidence that serine is cleaved by a retroaldol mechanism.

Related PDB

1rv3,1rv4,1rvu,1rvy

[48]

PubMed ID

15273312

Journal

Protein Sci

Year

2004

Volume

Pages

2184-95

Authors

Bhatt AN, Khan MY, Bhakuni V

Title

The C-terminal domain of dimeric serine hydroxymethyltransferase plays a key role in stabilization of the quaternary structure and cooperative unfolding of protein: domain swapping studies with enzymes having high sequence identity.

[49]

PubMed ID

15865438

Journal

Biochemistry

Year

2005

Volume

Pages

6929-37

Authors

Bhavani S, Trivedi V, Jala VR, Subramanya HS, Kaul P, Prakash V, Appaji Rao N, Savithri HS

Title

Role of Lys-226 in the catalytic mechanism of Bacillus stearothermophilus serine hydroxymethyltransferase--crystal structure and kinetic studies.

Related PDB

1yjs,1yjy,1yjz

[50]

PubMed ID

17651438

Journal

FEBS J

Year

2007

Volume

274

Pages

4148-60

Authors

Rajaram V, Bhavani BS, Kaul P, Prakash V, Appaji Rao N, Savithri HS, Murthy MR

Title

Structure determination and biochemical studies on Bacillus stearothermophilus E53Q serine hydroxymethyltransferase and its complexes provide insights on function and enzyme memory.

Related PDB

2vgt,2vgu,2vgv,2vgw

comments

This enzyme belongs to the type-I PLP-dependent enzyme superfamily (Aspartate aminotransferase superfamily, AAT; D00101 in EzCatDB).
There have been several possible catalytic mechanisms proposed for this enzyme (see [47]). Among these mechanisms, including the retro-aldol cleavage reaction (see [34], [38]) and the nucleophilic direct displacement reaction (see [38]), the concerted mechanism that combines the retro-aldol cleavage and the nucleophilic direct displacement reaction seems most likely (see [47], [50]).
This catalytic mechanism is composed of the following reactions:
(A) Formation of external aldimine (with amine group of L-Serine): Exchange of double-bonded atoms.
(B) SN1-like transfer of hydroxymethyl group from Ser-PLP to N5 of tetrahydrofolate (THF), forming a quinonoid intermediate of PLP-Gly (I00045) and a carbinolamine intermediate of THF (I00046).
(C) Elimination of hydroxyl group from the carbinolamine intermediate, forming an iminium cation intermediate of THF (I00047).
(D) Intramolecular addition of N10 to the carbon atom of the iminium cation.
(E or D') Isomerization (change in the position of double-bond), forming an external aldimine (Gly-PLP) from the quinonoid intermediate.
(F) Formation of internal aldimine, leading to the elimination of the product (Gly) from PLP: Exchange of double-bonded atoms.
These reactions proceed as follows:
(A) Formation of external aldimine (with amine group of L-Serine): Exchange of double-bonded atoms.
(A1) The negatively charged O3 atom of PLP modulates the pKa of the alpha-amino group of substrate, L-serine (Ser), and also the pKa of the internal aldimine with Lys229 (of 1dfo). Here, according to the literature from D00101 (D00101 [46], [59] & [61]), the imine-pyridine torsion (or strain) of PLP-Schiff base lowers pKa of the internal aldimine, without lowering pKa of the external aldimine. In any case, the difference in the pKa values facilitates the proton transfer from the alpha-amino group of Ser to the NZ nitrogen of Lys229. Moreover, the alpha-carboxylate of Ser may deprotonate the nucleophile, the alpha-amino group of Ser (see D00106 [10]).
(A2) The deprotonated amine group of Ser makes a nucleophilic attack on the C4' carbon of PLP, forming a transient geminal diamine intermediate.
(A3) There must be a general base, which deprotonates the amine group of the previously Ser substrate, so that the lone pair of the amine group can attack on the C4' atom to form a double-bond, and to release the amine of the catalytic residue, Lys229. Considering the active-site structure, Tyr55' (from the adjacent chain) may play the role as the general base, although the literature has not mentioned it (except for the literature from D00101 [11]). (The released Lys229 must be deprotonated, so that it can act as a general base at the final stage.) However, according to the active site structure of geminal diamine intermediate, the short distance between the NZ atom of Lys229 and amine group of the amino acid substrate suggests that a direct proton transfer can occur. Moreover, according to the literature [34], Thr226 stabilizes the unprotonated NZ atom of Lys229 (acting as a modulator).
(A4) The lone pair of the amine group (of Ser) makes a nucleophilic attack on the C4' atom to form a double-bond, releasing the amine of Lys229, leading to the formation of the external aldimine with L-Ser.
(B) Transfer of hydroxymethyl group from Ser-PLP to N5 of tetrahydrofolate (THF), forming a quinonoid intermediate of PLP-Gly (I00045) and a carbinolamine intermediate of THF (I00046).
(B1) Asp200 interacts with the N1 atom of PLP, modulating and enhancing the activity of the PLP cofactor as an electron sink, leading to polarization of the C2-C3 (or alpha-beta carbon atoms) bond, with positive charge accumulating on the C3 atom (see [47]; D00101 [17], [24]). The hydrogen-bond from Glu57 to O-gamma increases the charge on the C3 even further (Glu57 acting as a modulator?). Thus, the polarized C2-C3 bond is easily broken (see [47]).
(B2) A general base deprotonates the N5 atom of THF for its activation. (A water can be the weak base.)
(B3) The activated N5 atom makes a nucleophilic attack on the beta-carbon (or C3) atom of Ser-PLP, cleaving the C2-C3 bond to give a carbinolamine intermediate (I00046; THF-CH2OH) and a quinonoid intermediate of Gly-PLP (I00045). Asp200 may stabilize the quinonoid intermediate, through the interaction with the N1 atom of PLP (see D00271 [8]). This transfer reaction is an SN2-like reaction (see [47]).
(C) Elimination of hydroxyl group from the carbinolamine intermediate, forming an iminium cation intermediate of THF (I00047).
(C1) Glu57 acts as a general acid to protonate the hydroxyl group of the carbinolamine intermediate.
(C2) The hydroxyl group is eliminated from the intermediate to form a water molecule, forming a 5-iminium-THF (I00047).
(D) Intramolecular addition of N10 to the carbon atom of the iminium cation.
(D1) Glu57 acts as a general base to deprotonate the N10 atom (added group) of the iminium cation intermediate.
(D2) The activated the N10 atom makes a nucleophilic attack on the carbon atom of the iminium cation (addition site), forming a covalent bond with it.
(E or D') Isomerization (change in the position of double-bond), forming an external aldimine (Gly-PLP) from the quinonoid intermediate.
(E1) Although Tyr65' stabilizes the quinonoid intermediate (see [30]), it may act as a general acid to protonate the C2 atom of the quinonoid intermediate.
(E2) This reaction produces an external aldimine intermediate (I00044; Gly-PLP).
(F) Formation of internal aldimine, leading to the elimination of the product (Gly) from PLP: Exchange of double-bonded atoms.
(F1) Thr226 stabilizes the unprotonated NZ atom of Lys229 (acting as a modulator).
(F2) The deprotonated amine group of Lys229 makes a nucleophilic attack on the C4' carbon of the PLP of the external aldimine, forming a transient geminal diamine intermediate.
(F3) The lone pair of the amine nitrogen of Lys229 can attack on the C4' atom to form a double-bond, and to release the amine of the second product, Gly.
(F4) The negatively charged O3 atom of PLP modulates the pKa of the alpha-amino group of product, Gly, and also the pKa of the internal aldimine with Lys229. In any case, the difference in the pKa values facilitates the proton transfer from the NZ nitrogen of Lys229 to the alpha-amine group of Gly. The alpha-carboxylate of Gly may protonate the leaving group, the alpha-amino group of Gly (see D00106 [10]).

created

updated

2004-11-25

2009-02-26

Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )