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2vmr

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Revision as of 11:40, 30 March 2022

Crystal structure of Y60AbsSHMT internal aldimine

Structural highlights

2vmr is a 1 chain structure with sequence from Atcc 12980. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	1kkj, 1kkp, 1kl1, 1yjy, 1yjz, 2vgs, 2vgu, 2vi8, 2vi9, 2via, 2vib, 1kl2, 1yjs, 2vgt, 2vgv, 2vgw, 2vmn, 2vmo, 2vmp, 2vmq, 2vms, 2vmt, 2vmu, 2vmv, 2vmw, 2vmx, 2vmy, 2vmz
Activity:	Glycine hydroxymethyltransferase, with EC number 2.1.2.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[Q7SIB6_GEOSE] 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.[HAMAP-Rule:MF_00051]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

SHMT (serine hydoxymethyltransferase), a type I pyridoxal 5'-phosphate-dependent enzyme, catalyses the conversion of L-serine and THF (tetrahydrofolate) into glycine and 5,10-methylene THF. SHMT also catalyses several THF-independent side reactions such as cleavage of beta-hydroxy amino acids, transamination, racemization and decarboxylation. In the present study, the residues Asn(341), Tyr(60) and Phe(351), which are likely to influence THF binding, were mutated to alanine, alanine and glycine respectively, to elucidate the role of these residues in THF-dependent and -independent reactions catalysed by SHMT. The N341A and Y60A bsSHMT (Bacillus stearothermophilus SHMT) mutants were inactive for the THF-dependent activity, while the mutations had no effect on THF-independent activity. However, mutation of Phe(351) to glycine did not have any effect on either of the activities. The crystal structures of the glycine binary complexes of the mutants showed that N341A bsSHMT forms an external aldimine as in bsSHMT, whereas Y60A and F351G bsSHMTs exist as a mixture of internal/external aldimine and gem-diamine forms. Crystal structures of all of the three mutants obtained in the presence of L-allo-threonine were similar to the respective glycine binary complexes. The structure of the ternary complex of F351G bsSHMT with glycine and FTHF (5-formyl THF) showed that the monoglutamate side chain of FTHF is ordered in both the subunits of the asymmetric unit, unlike in the wild-type bsSHMT. The present studies demonstrate that the residues Asn(341) and Tyr(60) are pivotal for the binding of THF/FTHF, whereas Phe(351) is responsible for the asymmetric binding of FTHF in the two subunits of the dimer.

Structural and functional studies of Bacillus stearothermophilus serine hydroxymethyltransferase: the role of Asn(341), Tyr(60) and Phe(351) in tetrahydrofolate binding.,Pai VR, Rajaram V, Bisht S, Bhavani BS, Rao NA, Murthy MR, Savithri HS Biochem J. 2009 Mar 15;418(3):635-42. PMID:19046138^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Pai VR, Rajaram V, Bisht S, Bhavani BS, Rao NA, Murthy MR, Savithri HS. Structural and functional studies of Bacillus stearothermophilus serine hydroxymethyltransferase: the role of Asn(341), Tyr(60) and Phe(351) in tetrahydrofolate binding. Biochem J. 2009 Mar 15;418(3):635-42. PMID:19046138 doi:10.1042/BJ20081739

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vmr"

@@ Line 3: / Line 3: @@
 <StructureSection load='2vmr' size='340' side='right'caption='[[2vmr]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vmr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VMR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vmr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VMR FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kkj|1kkj]], [[1kkp|1kkp]], [[1kl1|1kl1]], [[1yjy|1yjy]], [[1yjz|1yjz]], [[2vgs|2vgs]], [[2vgu|2vgu]], [[2vi8|2vi8]], [[2vi9|2vi9]], [[2via|2via]], [[2vib|2vib]], [[1kl2|1kl2]], [[1yjs|1yjs]], [[2vgt|2vgt]], [[2vgv|2vgv]], [[2vgw|2vgw]], [[2vmn|2vmn]], [[2vmo|2vmo]], [[2vmp|2vmp]], [[2vmq|2vmq]], [[2vms|2vms]], [[2vmt|2vmt]], [[2vmu|2vmu]], [[2vmv|2vmv]], [[2vmw|2vmw]], [[2vmx|2vmx]], [[2vmy|2vmy]], [[2vmz|2vmz]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kkj|1kkj]], [[1kkp|1kkp]], [[1kl1|1kl1]], [[1yjy|1yjy]], [[1yjz|1yjz]], [[2vgs|2vgs]], [[2vgu|2vgu]], [[2vi8|2vi8]], [[2vi9|2vi9]], [[2via|2via]], [[2vib|2vib]], [[1kl2|1kl2]], [[1yjs|1yjs]], [[2vgt|2vgt]], [[2vgv|2vgv]], [[2vgw|2vgw]], [[2vmn|2vmn]], [[2vmo|2vmo]], [[2vmp|2vmp]], [[2vmq|2vmq]], [[2vms|2vms]], [[2vmt|2vmt]], [[2vmu|2vmu]], [[2vmv|2vmv]], [[2vmw|2vmw]], [[2vmx|2vmx]], [[2vmy|2vmy]], [[2vmz|2vmz]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2vmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vmr OCA], [http://pdbe.org/2vmr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vmr RCSB], [http://www.ebi.ac.uk/pdbsum/2vmr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vmr ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vmr OCA], [https://pdbe.org/2vmr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vmr RCSB], [https://www.ebi.ac.uk/pdbsum/2vmr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vmr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q7SIB6_GEOSE Q7SIB6_GEOSE]] 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.[HAMAP-Rule:MF_00051]
+[[https://www.uniprot.org/uniprot/Q7SIB6_GEOSE Q7SIB6_GEOSE]] 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.[HAMAP-Rule:MF_00051]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 ==See Also==
-*[[Serine hydroxymethyltransferase|Serine hydroxymethyltransferase]]
+*[[Serine hydroxymethyltransferase 3D structures|Serine hydroxymethyltransferase 3D structures]]
 == References ==
 <references/>

2vmr

From Proteopedia

Revision as of 11:40, 30 March 2022

Crystal structure of Y60AbsSHMT internal aldimine

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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