1rcq

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[[Image:1rcq.gif|left|200px]]
 
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{{Structure
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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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|PDB= 1rcq |SIZE=350|CAPTION= <scene name='initialview01'>1rcq</scene>, resolution 1.45&Aring;
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<StructureSection load='1rcq' size='340' side='right'caption='[[1rcq]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5&#39;-PHOSPHATE'>PLP</scene>
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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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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </span>
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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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|GENE= dadx ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])
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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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|DOMAIN=
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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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|RELATEDENTRY=[[1sft|1SFT]], [[1bdo|1BDO]], [[1epv|1EPV]], [[1l6f|1L6F]], [[2sfp|2SFP]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rcq OCA], [http://www.ebi.ac.uk/pdbsum/1rcq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rcq RCSB]</span>
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== Function ==
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}}
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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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==Overview==
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==See Also==
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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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*[[Alanine racemase 3D structures|Alanine racemase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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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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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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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 Sun Mar 30 23:26:20 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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