1j93

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure and Substrate Binding Modeling of the Uroporphyrinogen-III Decarboxylase from Nicotiana tabacum: Implications for the Catalytic Mechanism

Structural highlights

1j93 is a 1 chain structure with sequence from Nicotiana tabacum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DCUP_TOBAC Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III.[HAMAP-Rule:MF_00218]

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 enzymatic catalysis of many biological processes of life is supported by the presence of cofactors and prosthetic groups originating from the common tetrapyrrole precursor uroporphyrinogen-III. Uroporphyrinogen-III decarboxylase catalyzes its conversion into coproporphyrinogen-III, leading in plants to chlorophyll and heme biosynthesis. Here we report the first crystal structure of a plant (Nicotiana tabacum) uroporphyrinogen-III decarboxylase, together with the molecular modeling of substrate binding in tobacco and human enzymes. Its structural comparison with the homologous human protein reveals a similar catalytic cleft with six invariant polar residues, Arg(32), Arg(36), Asp(82), Ser(214) (Thr in Escherichia coli), Tyr(159), and His(329) (tobacco numbering). The functional relationships obtained from the structural and modeling analyses of both enzymes allowed the proposal for a refined catalytic mechanism. Asp(82) and Tyr(159) seem to be the catalytic functional groups, whereas the other residues may serve in substrate recognition and binding, with Arg(32) steering its insertion. The crystallographic dimer appears to represent the protein dimer under physiological conditions. The dimeric arrangement offers a plausible mechanism at least for the first two (out of four) decarboxylation steps.

Crystal structure and substrate binding modeling of the uroporphyrinogen-III decarboxylase from Nicotiana tabacum. Implications for the catalytic mechanism.,Martins BM, Grimm B, Mock HP, Huber R, Messerschmidt A J Biol Chem. 2001 Nov 23;276(47):44108-16. Epub 2001 Aug 27. PMID:11524417^[1]

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

References

↑ Martins BM, Grimm B, Mock HP, Huber R, Messerschmidt A. Crystal structure and substrate binding modeling of the uroporphyrinogen-III decarboxylase from Nicotiana tabacum. Implications for the catalytic mechanism. J Biol Chem. 2001 Nov 23;276(47):44108-16. Epub 2001 Aug 27. PMID:11524417 doi:http://dx.doi.org/10.1074/jbc.M104759200

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1j93"

@@ Line 3: / Line 3: @@
 <StructureSection load='1j93' size='340' side='right'caption='[[1j93]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1j93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/American_tobacco American tobacco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J93 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J93 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1j93]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nicotiana_tabacum Nicotiana tabacum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J93 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uroporphyrinogen_decarboxylase Uroporphyrinogen decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.37 4.1.1.37] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1j93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j93 OCA], [http://pdbe.org/1j93 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j93 RCSB], [http://www.ebi.ac.uk/pdbsum/1j93 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1j93 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=1j93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j93 OCA], [https://pdbe.org/1j93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j93 RCSB], [https://www.ebi.ac.uk/pdbsum/1j93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j93 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DCUP_TOBAC DCUP_TOBAC]] Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III.[HAMAP-Rule:MF_00218]
+[https://www.uniprot.org/uniprot/DCUP_TOBAC DCUP_TOBAC] Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III.[HAMAP-Rule:MF_00218]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j9/1j93_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: American tobacco]]
 [[Category: Large Structures]]
-[[Category: Uroporphyrinogen decarboxylase]]
+[[Category: Nicotiana tabacum]]
-[[Category: Grimm, B]]
+[[Category: Grimm B]]
-[[Category: Huber, R]]
+[[Category: Huber R]]
-[[Category: Martins, B M]]
+[[Category: Martins BM]]
-[[Category: Messerschmidt, A]]
+[[Category: Messerschmidt A]]
-[[Category: Mock, H P]]
+[[Category: Mock H-P]]
-[[Category: Beta barrel]]
-[[Category: Crystallographic dimer]]
-[[Category: Lyase]]
-[[Category: Plastidial enzyme]]

1j93

From Proteopedia

Current revision

Crystal Structure and Substrate Binding Modeling of the Uroporphyrinogen-III Decarboxylase from Nicotiana tabacum: Implications for the Catalytic Mechanism

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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