3dj8: Difference between revisions

Latest revision as of 15:10, 1 November 2023

Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I

Structural highlights

3dj8 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.51Å
Ligands:	EXY, MN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

ARGI1_HUMAN Defects in ARG1 are the cause of argininemia (ARGIN) [MIM:207800; also known as hyperargininemia. Argininemia is a rare autosomal recessive disorder of the urea cycle. Arginine is elevated in the blood and cerebrospinal fluid, and periodic hyperammonemia occurs. Clinical manifestations include developmental delay, seizures, mental retardation, hypotonia, ataxia, progressive spastic quadriplegia.^[1] ^[2]

Function

ARGI1_HUMAN

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

The synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid is reported along with the X-ray crystal structure of its complex with human arginase I, revealing unique coordination interactions with two manganese ions in the enzyme active site.

Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I.,Zakharian TY, Di Costanzo L, Christianson DW Org Biomol Chem. 2008 Sep 21;6(18):3240-3. Epub 2008 Aug 6. PMID:18802628^[3]

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

References

↑ Uchino T, Haraguchi Y, Aparicio JM, Mizutani N, Higashikawa M, Naitoh H, Mori M, Matsuda I. Three novel mutations in the liver-type arginase gene in three unrelated Japanese patients with argininemia. Am J Hum Genet. 1992 Dec;51(6):1406-12. PMID:1463019
↑ Uchino T, Snyderman SE, Lambert M, Qureshi IA, Shapira SK, Sansaricq C, Smit LM, Jakobs C, Matsuda I. Molecular basis of phenotypic variation in patients with argininemia. Hum Genet. 1995 Sep;96(3):255-60. PMID:7649538
↑ Zakharian TY, Di Costanzo L, Christianson DW. Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I. Org Biomol Chem. 2008 Sep 21;6(18):3240-3. Epub 2008 Aug 6. PMID:18802628 doi:10.1039/b811797g

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Uchino T, Haraguchi Y, Aparicio JM, Mizutani N, Higashikawa M, Naitoh H, Mori M, Matsuda I. Three novel mutations in the liver-type arginase gene in three unrelated Japanese patients with argininemia. Am J Hum Genet. 1992 Dec;51(6):1406-12. PMID:1463019

[2] Uchino T, Snyderman SE, Lambert M, Qureshi IA, Shapira SK, Sansaricq C, Smit LM, Jakobs C, Matsuda I. Molecular basis of phenotypic variation in patients with argininemia. Hum Genet. 1995 Sep;96(3):255-60. PMID:7649538

[3] Zakharian TY, Di Costanzo L, Christianson DW. Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I. Org Biomol Chem. 2008 Sep 21;6(18):3240-3. Epub 2008 Aug 6. PMID:18802628 doi:10.1039/b811797g

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='3dj8' size='340' side='right'caption='[[3dj8]], [[Resolution|resolution]] 1.51&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3dj8]] is a 2 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=3DJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3DJ8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3dj8]] is a 2 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=3DJ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DJ8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EXY:6-[(2R)-OXIRAN-2-YL]-L-NORLEUCINE'>EXY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.51&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2aeb|2aeb]], [[2zav|2zav]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EXY:6-[(2R)-OXIRAN-2-YL]-L-NORLEUCINE'>EXY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginase Arginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.1 3.5.3.1] </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=3dj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dj8 OCA], [https://pdbe.org/3dj8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dj8 RCSB], [https://www.ebi.ac.uk/pdbsum/3dj8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dj8 ProSAT]</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=3dj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dj8 OCA], [http://pdbe.org/3dj8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dj8 RCSB], [http://www.ebi.ac.uk/pdbsum/3dj8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dj8 ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/ARGI1_HUMAN ARGI1_HUMAN]] Defects in ARG1 are the cause of argininemia (ARGIN) [MIM:[http://omim.org/entry/207800 207800]]; also known as hyperargininemia. Argininemia is a rare autosomal recessive disorder of the urea cycle. Arginine is elevated in the blood and cerebrospinal fluid, and periodic hyperammonemia occurs. Clinical manifestations include developmental delay, seizures, mental retardation, hypotonia, ataxia, progressive spastic quadriplegia.<ref>PMID:1463019</ref> <ref>PMID:7649538</ref>
+[https://www.uniprot.org/uniprot/ARGI1_HUMAN ARGI1_HUMAN] Defects in ARG1 are the cause of argininemia (ARGIN) [MIM:[https://omim.org/entry/207800 207800]; also known as hyperargininemia. Argininemia is a rare autosomal recessive disorder of the urea cycle. Arginine is elevated in the blood and cerebrospinal fluid, and periodic hyperammonemia occurs. Clinical manifestations include developmental delay, seizures, mental retardation, hypotonia, ataxia, progressive spastic quadriplegia.<ref>PMID:1463019</ref> <ref>PMID:7649538</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/ARGI1_HUMAN ARGI1_HUMAN]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 38: @@
 __TOC__
 </StructureSection>
-[[Category: Arginase]]
+[[Category: Homo sapiens]]
-[[Category: Human]]
 [[Category: Large Structures]]
-[[Category: Christianson, D W]]
+[[Category: Christianson DW]]
-[[Category: Costanzo, L Di]]
+[[Category: Di Costanzo L]]
-[[Category: Arginine metabolism]]
-[[Category: Disease mutation]]
-[[Category: Epoxide binding]]
-[[Category: Hydrolase]]
-[[Category: Manganese]]
-[[Category: Manganese cluster]]
-[[Category: Metal-binding]]
-[[Category: Phosphoprotein]]
-[[Category: Urea cycle]]

3dj8: Difference between revisions

Latest revision as of 15:10, 1 November 2023

Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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