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[[Image:1pda.jpg|left|200px]]


{{Structure
==STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE==
|PDB= 1pda |SIZE=350|CAPTION= <scene name='initialview01'>1pda</scene>, resolution 1.76&Aring;
<StructureSection load='1pda' size='340' side='right'caption='[[1pda]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|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>
<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>
|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]  
</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>
|GENE=  
<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>
}}
<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>
</table>
== Function ==
[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]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pd/1pda_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


'''STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE'''
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:1522882<ref>PMID:1522882</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1pda" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
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.
*[[Porphobilinogen Deaminase|Porphobilinogen Deaminase]]
 
== References ==
==About this Structure==
<references/>
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].
__TOC__
 
</StructureSection>
==Reference==
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]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Hydroxymethylbilane synthase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Blundell TL]]
[[Category: Blundell, T L.]]
[[Category: Brownlie PD]]
[[Category: Brownlie, P D.]]
[[Category: Cooper JB]]
[[Category: Cooper, J B.]]
[[Category: Jordan PM]]
[[Category: Jordan, P M.]]
[[Category: Lambert R]]
[[Category: Lambert, R.]]
[[Category: Louie GV]]
[[Category: Louie, G V.]]
[[Category: Warren MJ]]
[[Category: Warren, M J.]]
[[Category: Wood SP]]
[[Category: Wood, S P.]]
[[Category: Woodcock SC]]
[[Category: Woodcock, S C.]]
[[Category: ACY]]
[[Category: DPM]]
[[Category: lyase(porphyrin)]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:22:56 2008''

Latest revision as of 22:10, 26 March 2025

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

1pda, resolution 1.76Å

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