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1pda

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[[Image:1pda.jpg|left|200px]]
 
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{{Structure
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==STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE==
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|PDB= 1pda |SIZE=350|CAPTION= <scene name='initialview01'>1pda</scene>, resolution 1.76&Aring;
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<StructureSection load='1pda' size='340' side='right'caption='[[1pda]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DPM:3-{2-[4-(2-CARBOXY-ETHYL)-3-CARBOXYMETHYL-5H-PYRROL-2-YLMETHYL]-4-CARBOXYMETHYL-5-METHYL-2H-PYRROL-3-YL}-PROPIONIC+ACID'>DPM</scene> and <scene name='pdbligand=ACY:ACETIC ACID'>ACY</scene>
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<table><tr><td colspan='2'>[[1pda]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PDA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PDA FirstGlance]. <br>
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|ACTIVITY= [http://en.wikipedia.org/wiki/Hydroxymethylbilane_synthase Hydroxymethylbilane synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.61 2.5.1.61]
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.76&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=DPM:3-[5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL-1H-PYRROL-2-YL]METHYL}-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC+ACID'>DPM</scene></td></tr>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pda OCA], [https://pdbe.org/1pda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pda RCSB], [https://www.ebi.ac.uk/pdbsum/1pda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pda ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/HEM3_ECOLI HEM3_ECOLI] Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps.[HAMAP-Rule:MF_00260]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pd/1pda_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pda ConSurf].
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<div style="clear:both"></div>
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'''STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE'''
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==See Also==
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*[[Porphobilinogen Deaminase|Porphobilinogen Deaminase]]
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__TOC__
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==Overview==
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</StructureSection>
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The three-domain structure of porphobilinogen deaminase, a key enzyme in the biosynthetic pathway of tetrapyrroles, has been defined by X-ray analysis at 1.9 A resolution. Two of the domains structurally resemble the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins. The X-ray structure and results from site-directed mutagenesis provide evidence for a single catalytic site. Interdomain flexibility may aid elongation of the polypyrrole product in the active-site cleft of the enzyme.
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==About this Structure==
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1PDA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PDA OCA].
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==Reference==
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Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site., Louie GV, Brownlie PD, Lambert R, Cooper JB, Blundell TL, Wood SP, Warren MJ, Woodcock SC, Jordan PM, Nature. 1992 Sep 3;359(6390):33-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1522882 1522882]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Hydroxymethylbilane synthase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Blundell TL]]
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[[Category: Blundell, T L.]]
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[[Category: Brownlie PD]]
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[[Category: Brownlie, P D.]]
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[[Category: Cooper JB]]
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[[Category: Cooper, J B.]]
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[[Category: Jordan PM]]
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[[Category: Jordan, P M.]]
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[[Category: Lambert R]]
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[[Category: Lambert, R.]]
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[[Category: Louie GV]]
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[[Category: Louie, G V.]]
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[[Category: Warren MJ]]
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[[Category: Warren, M J.]]
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[[Category: Wood SP]]
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[[Category: Wood, S P.]]
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[[Category: Woodcock SC]]
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[[Category: Woodcock, S C.]]
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[[Category: ACY]]
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[[Category: DPM]]
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[[Category: lyase(porphyrin)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:22:56 2008''
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Current revision

STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE

PDB ID 1pda

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