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1twi

From Proteopedia

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{{Seed}}
 
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[[Image:1twi.png|left|200px]]
 
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==Crystal structure of Diaminopimelate Decarboxylase from m. jannaschii in co-complex with L-lysine==
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The line below this paragraph, containing "STRUCTURE_1twi", creates the "Structure Box" on the page.
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<StructureSection load='1twi' size='340' side='right'caption='[[1twi]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1twi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TWI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TWI FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
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{{STRUCTURE_1twi| PDB=1twi | SCENE= }}
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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=1twi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1twi OCA], [https://pdbe.org/1twi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1twi RCSB], [https://www.ebi.ac.uk/pdbsum/1twi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1twi ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/1twi TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DCDA_METJA DCDA_METJA] Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.<ref>PMID:12429091</ref>
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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/tw/1twi_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=1twi ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Cocrystal structures of Methanococcus jannaschii diaminopimelate decarboxylase (DAPDC) bound to a substrate analog, azelaic acid, and its L-lysine product have been determined at 2.6 A and 2.0 A, respectively. This PLP-dependent enzyme is responsible for the final step of L-lysine biosynthesis in bacteria and plays a role in beta-lactam antibiotic resistance in Staphylococcus aureus. Substrate specificity derives from recognition of the L-chiral center of diaminopimelate and a system of ionic "molecular rulers" that dictate substrate length. A coupled-enzyme assay system permitted measurement of kinetic parameters for recombinant DAPDCs and inhibition constants (K(i)) for azelaic acid (89 microM) and other substrate analogs. Implications for rational design of broad-spectrum antimicrobial agents targeted against DAPDCs of drug-resistant strains of bacterial pathogens, such as Staphylococcus aureus, are discussed.
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===Crystal structure of Diaminopimelate Decarboxylase from m. jannaschii in co-complex with L-lysine===
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Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor.,Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK Structure. 2002 Nov;10(11):1499-508. PMID:12429091<ref>PMID:12429091</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_12429091}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1twi" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 12429091 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_12429091}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1TWI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TWI OCA].
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==Reference==
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Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor., Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK, Structure. 2002 Nov;10(11):1499-508. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12429091 12429091]
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[[Category: Diaminopimelate decarboxylase]]
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[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
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[[Category: Single protein]]
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[[Category: Bonanno JB]]
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[[Category: Bonanno, J B.]]
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[[Category: Burley SK]]
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[[Category: Burley, S K.]]
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[[Category: De Lencastre H]]
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[[Category: He, G.]]
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[[Category: He G]]
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[[Category: Lencastre, H De.]]
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[[Category: Pinho MG]]
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[[Category: NYSGXRC, New York Structural GenomiX Research Consortium.]]
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[[Category: Rajashankar KR]]
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[[Category: Pinho, M G.]]
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[[Category: Ray SS]]
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[[Category: Rajashankar, K R.]]
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[[Category: Tomasz A]]
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[[Category: Ray, S S.]]
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[[Category: Tomasz, A.]]
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[[Category: Antibiotic resistance]]
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[[Category: Diaminopimelate decarboxylase]]
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[[Category: Lysine biosynthesis]]
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[[Category: New york structural genomix research consortium]]
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[[Category: Nysgxrc]]
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[[Category: Protein structure initiative]]
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[[Category: Psi]]
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[[Category: Structural genomic]]
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[[Category: T135]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 14:38:01 2008''
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Current revision

Crystal structure of Diaminopimelate Decarboxylase from m. jannaschii in co-complex with L-lysine

PDB ID 1twi

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