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HAMAP rule MF_00051

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General rule information [?]

Accession MF_00051
Dates 1-JUN-2001 (Created)
7-MAY-2024 (Last updated, Version 61)
Name SHMT
Scope(s) Bacteria
Archaea
Template(s) 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 HAMAP; MF_00051 (Get profile general information and statistics)

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 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 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 Name=glyA;
else
Identifier GLYA
Protein name RecName: Full=Serine hydroxymethyltransferase;
                 Short=SHMT;
                 Short=Serine methylase;
                 EC=2.1.2.-;
Gene name Name=glyA;
end case

Comments [?]

case <OC:Bacteria> and <FT:5=H>
FUNCTIONCatalyzes 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 Reaction=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine; Xref=Rhea:RHEA:15481, ChEBI:CHEBI:15377, ChEBI:CHEBI:15636, ChEBI:CHEBI:33384, ChEBI:CHEBI:57305, ChEBI:CHEBI:57453; EC=2.1.2.1;
else case <OC:Bacteria> and <FT:5=T>
FUNCTIONCatalyzes the reversible interconversion of alpha-methyl-L- serine to D-alanine with tetrahydrofolate (THF) serving as the one- carbon carrier.
CATALYTIC ACTIVITY Reaction=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + D-alanine + H2O = (6S)-5,6,7,8-tetrahydrofolate + 2-methylserine; Xref=Rhea:RHEA:10064, ChEBI:CHEBI:15377, ChEBI:CHEBI:15636, ChEBI:CHEBI:57416, ChEBI:CHEBI:57453, ChEBI:CHEBI:58275; EC=2.1.2.7;
else case <OC:Bacteria> and not <FT:5>
FUNCTIONCatalyzes 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 Reaction=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine; Xref=Rhea:RHEA:15481, ChEBI:CHEBI:15377, ChEBI:CHEBI:15636, ChEBI:CHEBI:33384, ChEBI:CHEBI:57305, ChEBI:CHEBI:57453; EC=2.1.2.1;
else case <OC:Methanomicrobia> or <OC:Halobacteria>
FUNCTIONCatalyzes 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 Reaction=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine; Xref=Rhea:RHEA:15481, ChEBI:CHEBI:15377, ChEBI:CHEBI:15636, ChEBI:CHEBI:33384, ChEBI:CHEBI:57305, ChEBI:CHEBI:57453; EC=2.1.2.1;
else case <OC:Methanobacteria> or <OC:Methanococci> or <OC:Methanopyri> or <OC:Archaeoglobi>
FUNCTIONCatalyzes 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 Reaction=5,10-methylenetetrahydromethanopterin + glycine + H2O = 5,6,7,8-tetrahydromethanopterin + L-serine; Xref=Rhea:RHEA:47104, ChEBI:CHEBI:15377, ChEBI:CHEBI:33384, ChEBI:CHEBI:57305, ChEBI:CHEBI:57818, ChEBI:CHEBI:58103;
else
FUNCTIONCatalyzes 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 Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
case <OC:Bacteria> or <OC:Methanomicrobia> or <OC:Halobacteria>
PATHWAYOne-carbon metabolism; tetrahydrofolate interconversion.
end case
case <FT:5=H>
PATHWAYAmino-acid biosynthesis; glycine biosynthesis; glycine from L- serine: step 1/1.
end case
SUBUNITHomodimer.
SUBCELLULAR LOCATIONCytoplasm.
SIMILARITYBelongs 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
GO:0019264; Biological process:glycine biosynthetic process from serine
end case
case <OCellular component:Bacteria> or <OC:Methanomicrobia> or <OC:Halobacteria>
GO:0035999; Biological process:tetrahydrofolate interconversion
end case
GO:0030170; Molecular function:pyridoxal phosphate binding
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 125 127 /ligand="(6S)-5,6,7,8-tetrahydrofolate"
/ligand_id="ChEBI:CHEBI:57453"		 [GA]-H-[LIV]
BINDING 355 357 /ligand="(6S)-5,6,7,8-tetrahydrofolate"
/ligand_id="ChEBI:CHEBI:57453"		 [ST]-x-F
BINDING 121 121 /ligand="(6S)-5,6,7,8-tetrahydrofolate"
/ligand_id="ChEBI:CHEBI:57453"		 L
BINDING 246 246 /ligand="(6S)-5,6,7,8-tetrahydrofolate"
/ligand_id="ChEBI:CHEBI:57453"		 E
SITE 228 228 /note="Plays an important role in substrate specificity" [HT]
MOD_RES 229 229 /note="N6-(pyridoxal phosphate)lysine" K
case <OC:Escherichia> or <OC:Shigella>
MOD_RES 54 54 /note="N6-acetyllysine" acetylation K
MOD_RES 250 250 /note="N6-acetyllysine" acetylation K
MOD_RES 285 285 /note="N6-acetyllysine" acetylation K
MOD_RES 354 354 /note="N6-acetyllysine" acetylation K
MOD_RES 375 375 /note="N6-acetyllysine" acetylation K
end case

Additional information [?]

Size range 406-574 amino acids
Related rules None
Fusion Nter: None Cter: 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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