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3l0n

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Revision as of 07:04, 7 October 2020

Human orotidyl-5'-monophosphate decarboxylase in complex with 6-mercapto-UMP

Structural highlights

3l0n is a 2 chain structure with sequence from Human. This structure supersedes the now removed PDB entry 3ex5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	3l0k
Activity:	Orotidine-5'-phosphate decarboxylase, with EC number 4.1.1.23
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[UMPS_HUMAN] Defects in UMPS are the cause of orotic aciduria type 1 (ORAC1) [MIM:258900]. A disorder of pyrimidine metabolism resulting in megaloblastic anemia and orotic acid crystalluria that is frequently associated with some degree of physical and mental retardation. A minority of cases have additional features, particularly congenital malformations and immune deficiencies.^[1]

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

Orotidine-5'-monophosphate decarboxylase (OMPD) catalyzes the decarboxylation of orotidine-5'-monophosphate (OMP) to uridine-5'-monophosphate (UMP) in an extremely proficient manner. The reaction does not require any cofactors and proceeds by an unknown mechanism. In addition to decarboxylation, OMPD is able to catalyze other reactions. We show that several C6-substituted UMP derivatives undergo hydrolysis or substitution reactions that depend on a lysine residue (Lys314) in the OMPD active site. 6-Cyano-UMP is converted to UMP, and UMP derivatives with good leaving groups inhibit OMPD by a suicide mechanism in which Lys314 covalently binds to the substrate. These non-classical reactivities of human OMPD were characterized by cocrystallization and freeze-trapping experiments with wild-type OMPD and two active-site mutants by using substrate and inhibitor nucleotides. The structures show that the C6-substituents are not coplanar with the pyrimidine ring. The extent of this substrate distortion is a function of the substituent geometry. Structure-based mechanisms for the reaction of 6-substituted UMP derivatives are extracted in accordance with results from mutagenesis, mass spectrometry, and OMPD enzyme activity. The Lys314-based mechanisms explain the chemodiversity of OMPD, and offer a strategy to design mechanism-based inhibitors that could be used for antineoplastic purposes for example.

Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase.,Heinrich D, Diederichsen U, Rudolph MG Chemistry. 2009 Jul 6;15(27):6619-25. PMID:19472232^[2]

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

References

↑ Suchi M, Mizuno H, Kawai Y, Tsuboi T, Sumi S, Okajima K, Hodgson ME, Ogawa H, Wada Y. Molecular cloning of the human UMP synthase gene and characterization of point mutations in two hereditary orotic aciduria families. Am J Hum Genet. 1997 Mar;60(3):525-39. PMID:9042911
↑ Heinrich D, Diederichsen U, Rudolph MG. Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase. Chemistry. 2009 Jul 6;15(27):6619-25. PMID:19472232 doi:10.1002/chem.200900397

1 Structural highlights
2 Disease
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/3l0n"

@@ Line 1: / Line 1: @@
 ==Human orotidyl-5'-monophosphate decarboxylase in complex with 6-mercapto-UMP==
-<StructureSection load='3l0n' size='340' side='right' caption='[[3l0n]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
+<StructureSection load='3l0n' size='340' side='right'caption='[[3l0n]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3l0n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ex5 3ex5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L0N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L0N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3l0n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ex5 3ex5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L0N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3L0N FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=S5P:6-SULFANYLURIDINE-5-PHOSPHATE'>S5P</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=S5P:6-SULFANYLURIDINE-5-PHOSPHATE'>S5P</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3l0k|3l0k]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></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=3l0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l0n OCA], [http://pdbe.org/3l0n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3l0n RCSB], [http://www.ebi.ac.uk/pdbsum/3l0n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3l0n 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=3l0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l0n OCA], [http://pdbe.org/3l0n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3l0n RCSB], [http://www.ebi.ac.uk/pdbsum/3l0n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3l0n ProSAT]</span></td></tr>
 </table>
 == Disease ==
@@ Line 32: / Line 32: @@
 ==See Also==
-*[[Phosphoribosyltransferase|Phosphoribosyltransferase]]
+*[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]]
-*[[Uridine 5'-monophosphate synthase|Uridine 5'-monophosphate synthase]]
+*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]]
 == References ==
 <references/>
@@ Line 39: / Line 39: @@
 </StructureSection>
 [[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Orotidine-5'-phosphate decarboxylase]]
 [[Category: Diederichsen, U]]

3l0n

From Proteopedia

Revision as of 07:04, 7 October 2020

Human orotidyl-5'-monophosphate decarboxylase in complex with 6-mercapto-UMP

Structural highlights

Disease

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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