1rcq

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{{Seed}}
 
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[[Image:1rcq.png|left|200px]]
 
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==The 1.45 A crystal structure of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms==
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The line below this paragraph, containing "STRUCTURE_1rcq", creates the "Structure Box" on the page.
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<StructureSection load='1rcq' size='340' side='right'caption='[[1rcq]], [[Resolution|resolution]] 1.45&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'>[[1rcq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RCQ 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]] 1.45&#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=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
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{{STRUCTURE_1rcq| PDB=1rcq | 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=1rcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rcq OCA], [https://pdbe.org/1rcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rcq RCSB], [https://www.ebi.ac.uk/pdbsum/1rcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rcq ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ALR2_PSEAE ALR2_PSEAE] Isomerizes L-alanine to D-alanine which is then oxidized to pyruvate by DadA.<ref>PMID:10977898</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/rc/1rcq_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1rcq 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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The structure of the catabolic alanine racemase, DadX, from the pathogenic bacterium Pseudomonas aeruginosa, reported here at 1.45 A resolution, is a dimer in which each monomer is comprised of two domains, an eight-stranded alpha/beta barrel containing the PLP cofactor and a second domain primarily composed of beta-strands. The geometry of each domain is very similar to that of Bacillus stearothermophilus alanine racemase, but the rotation between domains differs by about 15 degrees. This change does not alter the structure of the active site in which almost all residues superimpose well with a low rms difference of 0.86 A. Unexpectedly, the active site of DadX contains a guest substrate that is located where acetate and propionate have been observed in the Bacillus structures. It is modeled as d-lysine and oriented such that its terminal NZ atom makes a covalent bond with C4' of PLP. Since the internal aldimine bond between the protein lysine, Lys33, and C4' of PLP is also unambiguously observed, there appears to be an equilibrium between both internally and externally reacted forms. The PLP cofactor adopts two partially occupied conformational states that resemble previously reported internal and external aldimine complexes.
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===The 1.45 A crystal structure of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms===
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Crystal structure at 1.45 A resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms.,LeMagueres P, Im H, Dvorak A, Strych U, Benedik M, Krause KL Biochemistry. 2003 Dec 23;42(50):14752-61. PMID:14674749<ref>PMID:14674749</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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<div class="pdbe-citations 1rcq" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_14674749}}, adds the Publication Abstract to the page
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*[[Alanine racemase 3D structures|Alanine racemase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 14674749 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_14674749}}
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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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1RCQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RCQ OCA].
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==Reference==
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Crystal structure at 1.45 A resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms., LeMagueres P, Im H, Dvorak A, Strych U, Benedik M, Krause KL, Biochemistry. 2003 Dec 23;42(50):14752-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14674749 14674749]
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[[Category: Alanine racemase]]
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[[Category: Pseudomonas aeruginosa]]
[[Category: Pseudomonas aeruginosa]]
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[[Category: Single protein]]
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[[Category: Benedik M]]
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[[Category: Benedik, M.]]
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[[Category: Dvorak A]]
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[[Category: Dvorak, A.]]
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[[Category: Im H]]
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[[Category: Im, H.]]
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[[Category: Krause KL]]
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[[Category: Krause, K L.]]
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[[Category: Le Magueres P]]
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[[Category: Magueres, P Le.]]
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[[Category: Strych U]]
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[[Category: Strych, U.]]
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[[Category: Alpha-beta barrel]]
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[[Category: Beta-structure for c-terminal domain]]
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[[Category: Internal/external aldimine form]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 20:02:59 2008''
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Current revision

The 1.45 A crystal structure of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms

PDB ID 1rcq

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