1ep1: Difference between revisions

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<StructureSection load='1ep1' size='340' side='right'caption='[[1ep1]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='1ep1' size='340' side='right'caption='[[1ep1]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ep1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_lactis"_lister_1873 "bacterium lactis" lister 1873]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EP1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1EP1 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1ep1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EP1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EP1 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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]] 2.2&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ep2|1ep2]], [[1ep3|1ep3]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotate_oxidase_(fumarate) Dihydroorotate oxidase (fumarate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.98.1 1.3.98.1] </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=1ep1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ep1 OCA], [https://pdbe.org/1ep1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ep1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ep1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ep1 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=1ep1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ep1 OCA], [http://pdbe.org/1ep1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ep1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ep1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ep1 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/PYRDB_LACLM PYRDB_LACLM]] Catalyzes the conversion of dihydroorotate to orotate with NAD(+) as electron acceptor. Can not use fumarate as an electron acceptor.<ref>PMID:8021180</ref> [[http://www.uniprot.org/uniprot/PYRK_LACLM PYRK_LACLM]] Responsible for channeling the electrons from the oxidation of dihydroorotate from the FMN redox center in the PyrDB subunit to the ultimate electron acceptor NAD(+).<ref>PMID:8910599</ref> 
[https://www.uniprot.org/uniprot/PYRDB_LACLM PYRDB_LACLM] Catalyzes the conversion of dihydroorotate to orotate with NAD(+) as electron acceptor. Can not use fumarate as an electron acceptor.<ref>PMID:8021180</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1ep1 ConSurf].
</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=1ep1 ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: The fourth step and only redox reaction in pyrimidine de novo biosynthesis is catalyzed by the flavoprotein dihydroorotate dehydrogenase (DHOD). Based on their sequences, DHODs are grouped into two major families. Lactococcus lactis is one of the few organisms with two DHODs, A and B, belonging to each of the two subgroups of family 1. The B enzyme (DHODB) is a prototype for DHODs in Gram-positive bacteria that use NAD+ as the second substrate. DHODB is a heterotetramer composed of two different proteins (PyrDB and PyrK) and three different cofactors: FMN, FAD, and a [2Fe-2S] cluster. RESULTS: Crystal structures have been determined for DHODB and its product complex. The DHODB heterotetramer is composed of two closely interacting PyrDB-PyrK dimers with the [2Fe-2S] cluster in their interface centered between the FMN and FAD groups. Conformational changes are observed between the complexed and uncomplexed state of the enzyme for the loop carrying the catalytic cysteine residue and one of the lysines interacting with FMN, which is important for substrate binding. CONCLUSIONS: A dimer of two PyrDB subunits resembling the family 1A enzymes forms the central core of DHODB. PyrK belongs to the NADPH ferredoxin reductase superfamily. The binding site for NAD+ has been deduced from the similarity to these proteins. The orotate binding in DHODB is similar to that in the family 1A enzymes. The close proximity of the three redox centers makes it possible to propose a possible electron transfer pathway involving residues conserved among the family 1B DHODs.
Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster.,Rowland P, Norager S, Jensen KF, Larsen S Structure. 2000 Dec 15;8(12):1227-38. PMID:11188687<ref>PMID:11188687</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ep1" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacterium lactis lister 1873]]
[[Category: Lactococcus lactis]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Jensen, K F]]
[[Category: Jensen KF]]
[[Category: Larsen, S]]
[[Category: Larsen S]]
[[Category: Norager, S]]
[[Category: Norager S]]
[[Category: Rowland, P]]
[[Category: Rowland P]]
[[Category: Heterotetramer]]
[[Category: Oxidoreductase]]

Latest revision as of 10:05, 7 February 2024

CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE BCRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B

Structural highlights

1ep1 is a 2 chain structure with sequence from Lactococcus lactis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PYRDB_LACLM Catalyzes the conversion of dihydroorotate to orotate with NAD(+) as electron acceptor. Can not use fumarate as an electron acceptor.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Andersen PS, Jansen PJ, Hammer K. Two different dihydroorotate dehydrogenases in Lactococcus lactis. J Bacteriol. 1994 Jul;176(13):3975-82. PMID:8021180

1ep1, resolution 2.20Å

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