4i8a: Difference between revisions

Revision as of 08:48, 9 November 2022

Alanine-glyoxylate aminotransferase variant S187F

Structural highlights

4i8a is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	GOL, LLP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

AGT1_HUMAN Primary hyperoxaluria type 1. The disease is caused by variants affecting the gene represented in this entry.

Function

AGT1_HUMAN Peroxisomal aminotransferase that catalyzes the transamination of glyoxylate to glycine and contributes to the glyoxylate detoxification (PubMed:10960483, PubMed:12777626, PubMed:24055001, PubMed:23229545, PubMed:26149463). Also catalyzes the transamination between L-serine and pyruvate and contributes to gluconeogenesis from the L-serine metabolism (PubMed:10347152).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

Biochemical Properties of the S187F Mutant AGT The substitution of Ser187, a residue located far from the active site of human liver peroxisomal alanine:glyoxylate aminotransferase (AGT), by Phe gives rise to a variant associated with primary hyperoxaluria type I (PH1). Unexpectedly, previous studies revealed that the recombinant form of S187F exhibits a remarkable loss of catalytic activity, an increased pyridoxal 5'-phosphate (PLP) binding affinity and a different coenzyme binding mode compared with normal AGT. To shed light on the structural elements responsible for these defects, we solved the crystal structure of the variant to a resolution of 2.9 A. Although the overall conformation of the variant is similar to that of normal AGT, we noticed: (i) a displacement of the PLP-binding Lys209 and Val185, located on the re and si side of PLP, respectively, and (ii) slight conformational changes of other active site residues, in particular Trp108, the base stacking residue with the pyridine cofactor moiety. This active site perturbation results in a mispositioning of the AGT-pyridoxamine 5'-phosphate (PMP) complex and of the external aldimine, as predicted by molecular modelling studies. Taken together, both predicted and observed movements caused by the S187F mutation are consistent with the following functional properties of the variant: (i) a 300-500-fold decrease in both the rate constant of L-alanine half-transamination and the kcat of the overall transamination, (ii) a different PMP binding mode and affinity, and (iii) a different microenvironment of the external aldimine. Proposals for the treatment of patients bearing S187F mutation are discussed on the basis of these results. (c) Proteins 2013;. (c) 2013 Wiley Periodicals, Inc.

Crystal structure of the S187F variant of human liver alanine: Glyoxylate aminotransferase associated with primary hyperoxaluria TYPE I and its functional implications.,Oppici E, Fodor K, Paiardini A, Williams C, Voltattorni CB, Willmanns M, Cellini B Proteins. 2013 Apr 15. doi: 10.1002/prot.24300. PMID:23589421^[7]

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

References

↑ Xue HH, Sakaguchi T, Fujie M, Ogawa H, Ichiyama A. Flux of the L-serine metabolism in rabbit, human, and dog livers. Substantial contributions of both mitochondrial and peroxisomal serine:pyruvate/alanine:glyoxylate aminotransferase. J Biol Chem. 1999 Jun 4;274(23):16028-33. doi: 10.1074/jbc.274.23.16028. PMID:10347152 doi:https://dx.doi.org/10.1074/jbc.274.23.16028
↑ Lumb MJ, Danpure CJ. Functional synergism between the most common polymorphism in human alanine:glyoxylate aminotransferase and four of the most common disease-causing mutations. J Biol Chem. 2000 Nov 17;275(46):36415-22. PMID:10960483 doi:10.1074/jbc.M006693200
↑ Santana A, Salido E, Torres A, Shapiro LJ. Primary hyperoxaluria type 1 in the Canary Islands: a conformational disease due to I244T mutation in the P11L-containing alanine:glyoxylate aminotransferase. Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7277-82. Epub 2003 May 30. PMID:12777626 doi:10.1073/pnas.1131968100
↑ Fargue S, Lewin J, Rumsby G, Danpure CJ. Four of the most common mutations in primary hyperoxaluria type 1 unmask the cryptic mitochondrial targeting sequence of alanine:glyoxylate aminotransferase encoded by the polymorphic minor allele. J Biol Chem. 2013 Jan 25;288(4):2475-84. doi: 10.1074/jbc.M112.432617. Epub 2012 , Dec 10. PMID:23229545 doi:https://dx.doi.org/10.1074/jbc.M112.432617
↑ Oppici E, Roncador A, Montioli R, Bianconi S, Cellini B. Gly161 mutations associated with Primary Hyperoxaluria Type I induce the cytosolic aggregation and the intracellular degradation of the apo-form of alanine:glyoxylate aminotransferase. Biochim Biophys Acta. 2013 Dec;1832(12):2277-88. doi:, 10.1016/j.bbadis.2013.09.002. Epub 2013 Sep 17. PMID:24055001 doi:https://dx.doi.org/10.1016/j.bbadis.2013.09.002
↑ Montioli R, Oppici E, Dindo M, Roncador A, Gotte G, Cellini B, Borri Voltattorni C. Misfolding caused by the pathogenic mutation G47R on the minor allele of alanine:glyoxylate aminotransferase and chaperoning activity of pyridoxine. Biochim Biophys Acta. 2015 Oct;1854(10 Pt A):1280-9. doi:, 10.1016/j.bbapap.2015.07.002. Epub 2015 Jul 3. PMID:26149463 doi:https://dx.doi.org/10.1016/j.bbapap.2015.07.002
↑ Oppici E, Fodor K, Paiardini A, Williams C, Voltattorni CB, Willmanns M, Cellini B. Crystal structure of the S187F variant of human liver alanine: Glyoxylate aminotransferase associated with primary hyperoxaluria TYPE I and its functional implications. Proteins. 2013 Apr 15. doi: 10.1002/prot.24300. PMID:23589421 doi:10.1002/prot.24300

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Xue HH, Sakaguchi T, Fujie M, Ogawa H, Ichiyama A. Flux of the L-serine metabolism in rabbit, human, and dog livers. Substantial contributions of both mitochondrial and peroxisomal serine:pyruvate/alanine:glyoxylate aminotransferase. J Biol Chem. 1999 Jun 4;274(23):16028-33. doi: 10.1074/jbc.274.23.16028. PMID:10347152 doi:https://dx.doi.org/10.1074/jbc.274.23.16028

[2] Lumb MJ, Danpure CJ. Functional synergism between the most common polymorphism in human alanine:glyoxylate aminotransferase and four of the most common disease-causing mutations. J Biol Chem. 2000 Nov 17;275(46):36415-22. PMID:10960483 doi:10.1074/jbc.M006693200

[3] Santana A, Salido E, Torres A, Shapiro LJ. Primary hyperoxaluria type 1 in the Canary Islands: a conformational disease due to I244T mutation in the P11L-containing alanine:glyoxylate aminotransferase. Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7277-82. Epub 2003 May 30. PMID:12777626 doi:10.1073/pnas.1131968100

[4] Fargue S, Lewin J, Rumsby G, Danpure CJ. Four of the most common mutations in primary hyperoxaluria type 1 unmask the cryptic mitochondrial targeting sequence of alanine:glyoxylate aminotransferase encoded by the polymorphic minor allele. J Biol Chem. 2013 Jan 25;288(4):2475-84. doi: 10.1074/jbc.M112.432617. Epub 2012 , Dec 10. PMID:23229545 doi:https://dx.doi.org/10.1074/jbc.M112.432617

[5] Oppici E, Roncador A, Montioli R, Bianconi S, Cellini B. Gly161 mutations associated with Primary Hyperoxaluria Type I induce the cytosolic aggregation and the intracellular degradation of the apo-form of alanine:glyoxylate aminotransferase. Biochim Biophys Acta. 2013 Dec;1832(12):2277-88. doi:, 10.1016/j.bbadis.2013.09.002. Epub 2013 Sep 17. PMID:24055001 doi:https://dx.doi.org/10.1016/j.bbadis.2013.09.002

[6] Montioli R, Oppici E, Dindo M, Roncador A, Gotte G, Cellini B, Borri Voltattorni C. Misfolding caused by the pathogenic mutation G47R on the minor allele of alanine:glyoxylate aminotransferase and chaperoning activity of pyridoxine. Biochim Biophys Acta. 2015 Oct;1854(10 Pt A):1280-9. doi:, 10.1016/j.bbapap.2015.07.002. Epub 2015 Jul 3. PMID:26149463 doi:https://dx.doi.org/10.1016/j.bbapap.2015.07.002

[7] Oppici E, Fodor K, Paiardini A, Williams C, Voltattorni CB, Willmanns M, Cellini B. Crystal structure of the S187F variant of human liver alanine: Glyoxylate aminotransferase associated with primary hyperoxaluria TYPE I and its functional implications. Proteins. 2013 Apr 15. doi: 10.1002/prot.24300. PMID:23589421 doi:10.1002/prot.24300

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@@ Line 1: / Line 1: @@
 ==Alanine-glyoxylate aminotransferase variant S187F==
-<StructureSection load='4i8a' size='340' side='right' caption='[[4i8a]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='4i8a' size='340' side='right'caption='[[4i8a]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4i8a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I8A FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4i8a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I8A FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></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=4i8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8a OCA], [https://pdbe.org/4i8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i8a RCSB], [https://www.ebi.ac.uk/pdbsum/4i8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i8a ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1h0c|1h0c]], [[1jo4|1jo4]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AGXT, AGT1, SPAT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4i8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8a OCA], [http://pdbe.org/4i8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i8a RCSB], [http://www.ebi.ac.uk/pdbsum/4i8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i8a ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/SPYA_HUMAN SPYA_HUMAN]] Defects in AGXT are the cause of hyperoxaluria primary type 1 (HP1) [MIM:[http://omim.org/entry/259900 259900]]; also known as primary hyperoxaluria type I (PH1) and oxalosis I. HP1 is a rare autosomal recessive inborn error of glyoxylate metabolism characterized by increased excretion of oxalate and glycolate, and the progressive accumulation of insoluble calcium oxalate in the kidney and urinary tract.<ref>PMID:1703535</ref> <ref>PMID:2039493</ref> <ref>PMID:1349575</ref> <ref>PMID:1301173</ref> <ref>PMID:8101040</ref> <ref>PMID:9192270</ref> <ref>PMID:9604803</ref> <ref>PMID:10394939</ref> <ref>PMID:10453743</ref> <ref>PMID:10541294</ref> <ref>PMID:10862087</ref> <ref>PMID:10960483</ref> <ref>PMID:12559847</ref> <ref>PMID:12777626</ref> <ref>PMID:15253729</ref> <ref>PMID:15849466</ref> <ref>PMID:15961946</ref> <ref>PMID:15963748</ref>
+[https://www.uniprot.org/uniprot/AGT1_HUMAN AGT1_HUMAN] Primary hyperoxaluria type 1. The disease is caused by variants affecting the gene represented in this entry.
+== Function ==
+[https://www.uniprot.org/uniprot/AGT1_HUMAN AGT1_HUMAN] Peroxisomal aminotransferase that catalyzes the transamination of glyoxylate to glycine and contributes to the glyoxylate detoxification (PubMed:10960483, PubMed:12777626, PubMed:24055001, PubMed:23229545, PubMed:26149463). Also catalyzes the transamination between L-serine and pyruvate and contributes to gluconeogenesis from the L-serine metabolism (PubMed:10347152).<ref>PMID:10347152</ref> <ref>PMID:10960483</ref> <ref>PMID:12777626</ref> <ref>PMID:23229545</ref> <ref>PMID:24055001</ref> <ref>PMID:26149463</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 22: @@
 ==See Also==
-*[[Aminotransferase|Aminotransferase]]
+*[[Aminotransferase 3D structures|Aminotransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Cellini, B]]
+[[Category: Large Structures]]
-[[Category: Fodor, K]]
+[[Category: Cellini B]]
-[[Category: Oppici, E]]
+[[Category: Fodor K]]
-[[Category: Williams, C]]
+[[Category: Oppici E]]
-[[Category: Wilmanns, M]]
+[[Category: Williams C]]
-[[Category: Aminotransferase]]
+[[Category: Wilmanns M]]
-[[Category: Peroxisome]]
-[[Category: Primary hyperoxaluria type 1]]
-[[Category: Transferase]]

4i8a: Difference between revisions

Revision as of 08:48, 9 November 2022

Alanine-glyoxylate aminotransferase variant S187F

Structural highlights

Disease

Function

Publication Abstract from PubMed

See Also

References

Contents

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