1niu

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[[Image:1niu.gif|left|200px]]
 
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{{Structure
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==ALANINE RACEMASE WITH BOUND INHIBITOR DERIVED FROM L-CYCLOSERINE==
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|PDB= 1niu |SIZE=350|CAPTION= <scene name='initialview01'>1niu</scene>, resolution 2.20&Aring;
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<StructureSection load='1niu' size='340' side='right'caption='[[1niu]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DCS:D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE'>DCS</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>
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<table><tr><td colspan='2'>[[1niu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NIU 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]] 2.2&#8491;</td></tr>
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|GENE= ALR OR DAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCS:D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE'>DCS</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</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=1niu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1niu OCA], [https://pdbe.org/1niu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1niu RCSB], [https://www.ebi.ac.uk/pdbsum/1niu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1niu ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1sft|1SFT]], [[1bd0|1BD0]], [[1epv|1EPV]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1niu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1niu OCA], [http://www.ebi.ac.uk/pdbsum/1niu PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1niu RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/ALR_GEOSE ALR_GEOSE] Catalyzes the interconversion of L-alanine and D-alanine. Also weakly active on serine.<ref>PMID:10502689</ref> <ref>PMID:12203980</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/ni/1niu_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=1niu 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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Alanine racemase (EC 5.1.1.1) catalyzes the interconversion of alanine enantiomers, and thus represents the first committed step involved in bacterial cell wall biosynthesis. Cycloserine acts as a suicide inhibitor of alanine racemase and as such, serves as an antimicrobial agent. The chemical means by which cycloserine inhibits alanine racemase is unknown. Through spectroscopic assays, we show here evidence of a pyridoxal derivative (arising from either isomer of cycloserine) saturated at the C4' carbon position. We additionally report the L- and D-cycloserine inactivated crystal structures of Bacillus stearothermophilus alanine racemase, which corroborates the spectroscopy via evidence of a 3-hydroxyisoxazole pyridoxamine derivative. Upon the basis of the kinetic and structural properties of both the L- and D-isomers of the inhibitor, we propose a mechanism of alanine racemase inactivation by cycloserine. This pathway involves an initial transamination step followed by tautomerization to form a stable aromatic adduct, a scheme similar to that seen in cycloserine inactivation of aminotransferases.
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'''ALANINE RACEMASE WITH BOUND INHIBITOR DERIVED FROM L-CYCLOSERINE'''
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A side reaction of alanine racemase: transamination of cycloserine.,Fenn TD, Stamper GF, Morollo AA, Ringe D Biochemistry. 2003 May 20;42(19):5775-83. PMID:12741835<ref>PMID:12741835</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 1niu" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Alanine racemase (EC 5.1.1.1) catalyzes the interconversion of alanine enantiomers, and thus represents the first committed step involved in bacterial cell wall biosynthesis. Cycloserine acts as a suicide inhibitor of alanine racemase and as such, serves as an antimicrobial agent. The chemical means by which cycloserine inhibits alanine racemase is unknown. Through spectroscopic assays, we show here evidence of a pyridoxal derivative (arising from either isomer of cycloserine) saturated at the C4' carbon position. We additionally report the L- and D-cycloserine inactivated crystal structures of Bacillus stearothermophilus alanine racemase, which corroborates the spectroscopy via evidence of a 3-hydroxyisoxazole pyridoxamine derivative. Upon the basis of the kinetic and structural properties of both the L- and D-isomers of the inhibitor, we propose a mechanism of alanine racemase inactivation by cycloserine. This pathway involves an initial transamination step followed by tautomerization to form a stable aromatic adduct, a scheme similar to that seen in cycloserine inactivation of aminotransferases.
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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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1NIU is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIU OCA].
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__TOC__
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</StructureSection>
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==Reference==
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A side reaction of alanine racemase: transamination of cycloserine., Fenn TD, Stamper GF, Morollo AA, Ringe D, Biochemistry. 2003 May 20;42(19):5775-83. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12741835 12741835]
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[[Category: Alanine racemase]]
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[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Fenn, T D.]]
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[[Category: Fenn TD]]
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[[Category: Morollo, A A.]]
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[[Category: Morollo AA]]
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[[Category: Ringe, D.]]
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[[Category: Ringe D]]
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[[Category: Stamper, G F.]]
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[[Category: Stamper GF]]
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[[Category: plp-containing]]
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[[Category: tim barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:30:57 2008''
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Current revision

ALANINE RACEMASE WITH BOUND INHIBITOR DERIVED FROM L-CYCLOSERINE

PDB ID 1niu

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