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2w7i

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Revision as of 10:59, 6 April 2022

Crystal structure of Y61AbsSHMT internal aldimine

Structural highlights

2w7i 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:	1yjy, 2w7f, 2vmv, 1yjz, 2vgv, 2vmy, 2vi9, 2vmu, 1kl1, 1kkp, 1kkj, 2vmx, 2w7e, 1kl2, 2vmz, 2w7g, 2vib, 2vgs, 2vms, 2vmt, 2vmn, 2vmp, 2vmr, 2vgu, 1yjs, 2w7d, 2vi8, 2vgt, 2via, 2vmq, 2vmw, 2vmo, 2vgw, 2w7j, 2w7m, 2w7l, 2w7h, 2w7k
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

Serine hydroxymethyltransferase (SHMT) from Bacillus stearothermophilus (bsSHMT) is a pyridoxal 5'-phosphate-dependent enzyme that catalyses the conversion of L-serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. In addition, the enzyme catalyses the tetrahydrofolate-independent cleavage of 3-hydroxy amino acids and transamination. In this article, we have examined the mechanism of the tetrahydrofolate-independent cleavage of 3-hydroxy amino acids by SHMT. The three-dimensional structure and biochemical properties of Y51F and Y61A bsSHMTs and their complexes with substrates, especially L-allo-Thr, show that the cleavage of 3-hydroxy amino acids could proceed via Calpha proton abstraction rather than hydroxyl proton removal. Both mutations result in a complete loss of tetrahydrofolate-dependent and tetrahydrofolate-independent activities. The mutation of Y51 to F strongly affects the binding of pyridoxal 5'-phosphate, possibly as a consequence of a change in the orientation of the phenyl ring in Y51F bsSHMT. The mutant enzyme could be completely reconstituted with pyridoxal 5'-phosphate. However, there was an alteration in the lambda max value of the internal aldimine (396 nm), a decrease in the rate of reduction with NaCNBH3 and a loss of the intermediate in the interaction with methoxyamine (MA). The mutation of Y61 to A results in the loss of interaction with Calpha and Cbeta of the substrates. X-Ray structure and visible CD studies show that the mutant is capable of forming an external aldimine. However, the formation of the quinonoid intermediate is hindered. It is suggested that Y61 is involved in the abstraction of the Calpha proton from 3-hydroxy amino acids. A new mechanism for the cleavage of 3-hydroxy amino acids via Calpha proton abstraction by SHMT is proposed.

Importance of tyrosine residues of Bacillus stearothermophilus serine hydroxymethyltransferase in cofactor binding and L-allo-Thr cleavage.,Bhavani BS, Rajaram V, Bisht S, Kaul P, Prakash V, Murthy MR, Appaji Rao N, Savithri HS FEBS J. 2008 Sep;275(18):4606-19. Epub 2008 Aug 11. PMID:18699779^[1]

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

References

↑ Bhavani BS, Rajaram V, Bisht S, Kaul P, Prakash V, Murthy MR, Appaji Rao N, Savithri HS. Importance of tyrosine residues of Bacillus stearothermophilus serine hydroxymethyltransferase in cofactor binding and L-allo-Thr cleavage. FEBS J. 2008 Sep;275(18):4606-19. Epub 2008 Aug 11. PMID:18699779 doi:10.1111/j.1742-4658.2008.06603.x

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/2w7i"

@@ Line 3: / Line 3: @@
 <StructureSection load='2w7i' size='340' side='right'caption='[[2w7i]], [[Resolution|resolution]] 2.72&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2w7i]] 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=2W7I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2W7I FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2w7i]] 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=2W7I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W7I FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1yjy|1yjy]], [[2w7f|2w7f]], [[2vmv|2vmv]], [[1yjz|1yjz]], [[2vgv|2vgv]], [[2vmy|2vmy]], [[2vi9|2vi9]], [[2vmu|2vmu]], [[1kl1|1kl1]], [[1kkp|1kkp]], [[1kkj|1kkj]], [[2vmx|2vmx]], [[2w7e|2w7e]], [[1kl2|1kl2]], [[2vmz|2vmz]], [[2w7g|2w7g]], [[2vib|2vib]], [[2vgs|2vgs]], [[2vms|2vms]], [[2vmt|2vmt]], [[2vmn|2vmn]], [[2vmp|2vmp]], [[2vmr|2vmr]], [[2vgu|2vgu]], [[1yjs|1yjs]], [[2w7d|2w7d]], [[2vi8|2vi8]], [[2vgt|2vgt]], [[2via|2via]], [[2vmq|2vmq]], [[2vmw|2vmw]], [[2vmo|2vmo]], [[2vgw|2vgw]], [[2w7j|2w7j]], [[2w7m|2w7m]], [[2w7l|2w7l]], [[2w7h|2w7h]], [[2w7k|2w7k]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yjy|1yjy]], [[2w7f|2w7f]], [[2vmv|2vmv]], [[1yjz|1yjz]], [[2vgv|2vgv]], [[2vmy|2vmy]], [[2vi9|2vi9]], [[2vmu|2vmu]], [[1kl1|1kl1]], [[1kkp|1kkp]], [[1kkj|1kkj]], [[2vmx|2vmx]], [[2w7e|2w7e]], [[1kl2|1kl2]], [[2vmz|2vmz]], [[2w7g|2w7g]], [[2vib|2vib]], [[2vgs|2vgs]], [[2vms|2vms]], [[2vmt|2vmt]], [[2vmn|2vmn]], [[2vmp|2vmp]], [[2vmr|2vmr]], [[2vgu|2vgu]], [[1yjs|1yjs]], [[2w7d|2w7d]], [[2vi8|2vi8]], [[2vgt|2vgt]], [[2via|2via]], [[2vmq|2vmq]], [[2vmw|2vmw]], [[2vmo|2vmo]], [[2vgw|2vgw]], [[2w7j|2w7j]], [[2w7m|2w7m]], [[2w7l|2w7l]], [[2w7h|2w7h]], [[2w7k|2w7k]]</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=2w7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w7i OCA], [http://pdbe.org/2w7i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w7i RCSB], [http://www.ebi.ac.uk/pdbsum/2w7i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2w7i 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=2w7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w7i OCA], [https://pdbe.org/2w7i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w7i RCSB], [https://www.ebi.ac.uk/pdbsum/2w7i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w7i 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/>

2w7i

From Proteopedia

Revision as of 10:59, 6 April 2022

Crystal structure of Y61AbsSHMT internal aldimine

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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