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HAMAP rule MF_00051

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General rule information [?]

Accession MF_00051
Dates 1-JUN-2001 (Created)
19-NOV-2022 (Last updated, Version 59)
Name SHMT
Scope
Bacteria
Archaea
Templates P0A825 (GLYA_ECOLI); D3DKC4 (GLYA_HYDTT); P9WGI9 (GLYA1_MYCTU); P9WGI7 (GLYA2_MYCTU); P39148 (GLYA_BACSU); Q58992 (GLYA_METJA); Q46A52 (GLYA_METBF); Q9UWT5 (GLYA_SACS2); O27433 (GLYA_METTH); B2DEU7 (MSHMT_PARSX): [Recover all]
Triggered by

Propagated annotation [?]


Identifier, protein and gene names [?]

case (<OC:Bacteria> and <FT:5=H>) or <OC:Methanomicrobia> or <OC:Halobacteria>
Identifier
GLYA
Protein name
RecName: Full=Serine hydroxymethyltransferase;
Short=SHMT;
Short=Serine methylase;
EC 2.1.2.1;
Gene name
glyA
else case <OC:Bacteria> and <FT:5=T>
Identifier
MSHMT
Protein name
RecName: Full=2-methylserine hydroxymethyltransferase;
Short=MSHMT;
EC 2.1.2.7;
AltName: Full=Alpha-methylserine hydroxymethyltransferase;
AltName: Full=D-alanine 2-hydroxymethyltransferase;
Gene name
mshmt
else case <OC:Bacteria> and not <FT:5>
Identifier
GLYA
Protein name
RecName: Full=Probable serine hydroxymethyltransferase;
Short=SHMT;
Short=Serine methylase;
EC 2.1.2.1;
Gene name
glyA
else
Identifier
GLYA
Protein name
RecName: Full=Serine hydroxymethyltransferase;
Short=SHMT;
Short=Serine methylase;
EC 2.1.2.-;
Gene name
glyA
end case

Comments [?]

case <OC:Bacteria> and <FT:5=H>
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.
Catalytic activity RHEA:15481: (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine
EC 2.1.2.1
else case <OC:Bacteria> and <FT:5=T>
Function Catalyzes the reversible interconversion of alpha-methyl-L-serine to D-alanine with tetrahydrofolate (THF) serving as the one-carbon carrier.
Catalytic activity RHEA:10064: (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + D-alanine + H2O = (6S)-5,6,7,8-tetrahydrofolate + 2-methylserine
EC 2.1.2.7
else case <OC:Bacteria> and not <FT:5>
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.
Catalytic activity RHEA:15481: (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine
EC 2.1.2.1
else case <OC:Methanomicrobia> or <OC:Halobacteria>
Function Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.
Catalytic activity RHEA:15481: (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine
EC 2.1.2.1
else case <OC:Methanobacteria> or <OC:Methanococci> or <OC:Methanopyri> or <OC:Archaeoglobi>
Function Catalyzes the reversible interconversion of serine and glycine with tetrahydromethanopterin (H4MPT) serving as the one-carbon carrier. Also exhibits a pteridine-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.
Catalytic activity RHEA:47104: 5,10-methylenetetrahydromethanopterin + glycine + H2O = 5,6,7,8-tetrahydromethanopterin + L-serine
else
Function Catalyzes the reversible interconversion of serine and glycine with a modified folate serving as the one-carbon carrier. Also exhibits a pteridine-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.
end case
Cofactor pyridoxal 5'-phosphate
case <OC:Bacteria> or <OC:Methanomicrobia> or <OC:Halobacteria>
Pathway One-carbon metabolism; tetrahydrofolate interconversion.
end case
case <FT:5=H>
Pathway Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1.
end case
Subunit Homodimer.
Subcellular location Cytoplasm.
Similarity Belongs to the SHMT family.

Keywords [?]

case <FTTag:acetylation>
Acetylation
end case
case <FT:5=H>
Amino-acid biosynthesis
end case
Cytoplasm
One-carbon metabolism
Pyridoxal phosphate
Transferase

Gene Ontology [?]

case <FT:5=H>
GO:0004372; Molecular function: glycine hydroxymethyltransferase activity.
end case
GO:0030170; Molecular function: pyridoxal phosphate binding.
GO:0006730; Biological process: one-carbon metabolic process.
case <FT:5=H>
GO:0019264; Biological process: glycine biosynthetic process from serine.
end case
GO:0005737; Cellular component: cytoplasm.

Cross-references [?]

Pfam PF00464; SHMT; 1;
PROSITE PS00096; SHMT; 1;
PIRSF PIRSF000412; SHMT; 1;

Features [?]

From: GLYA_ECOLI (P0A825)
Key     From     To       Description   Tag   Condition   FTGroup
BINDING (Optional)     125     127       /ligand="(6S)-5,6,7,8-tetrahydrofolate" /ligand_id="ChEBI:CHEBI:57453     [GA]-H-[LIV]  
BINDING (Optional)     355     357       /ligand="(6S)-5,6,7,8-tetrahydrofolate" /ligand_id="ChEBI:CHEBI:57453     [ST]-x-F  
BINDING (Optional)     121     121       /ligand="(6S)-5,6,7,8-tetrahydrofolate" /ligand_id="ChEBI:CHEBI:57453     L  
BINDING (Optional)     246     246       /ligand="(6S)-5,6,7,8-tetrahydrofolate" /ligand_id="ChEBI:CHEBI:57453     E  
SITE     228     228       Plays an important role in substrate specificity     [HT]  
MOD_RES     229     229       N6-(pyridoxal phosphate)lysine     K  
case <OC:Escherichia> or <OC:Shigella>
MOD_RES     54     54       N6-acetyllysine   acetylation   K  
MOD_RES     250     250       N6-acetyllysine   acetylation   K  
MOD_RES     285     285       N6-acetyllysine   acetylation   K  
MOD_RES     354     354       N6-acetyllysine   acetylation   K  
MOD_RES     375     375       N6-acetyllysine   acetylation   K  
end case

Additional information [?]

Size range 406-574 amino acids
Related rules None
Fusion None
Comments The pteridine substrate used in this reaction by Archaea differs depending on the species. Methanomicrobia and Halobacteria appear to use tetrahydrofolate, whereas Methanobacteria and Methanococci use tetrahydromethanopterin, Sulfolobus solfataricus use tetrahydrosulfopterin, and hyperthermophiles use a modified folate (see PMID: 9783425 and references mentioned in template entries). M.tuberculosis possesses 2 SHMTs, one (O53441, Rv1093) binds 1 pyridoxal phosphate per homodimer whereas the other (O53615, Rv0070c) binds 1 pyridoxal phosphate per subunit like other characterized members of the SHMT family. Possible wrong start in ARCFU. Possible C-terminal problem in TREPA.


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