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KEGG ENZYME: 4.2.1.168
<!doctype html> <html><head> <title>KEGG ENZYME: 4.2.1.168</title> <link type="text/css" rel="stylesheet" href="/css/gn2.css?1744241634"> <link type="text/css" rel="stylesheet" href="/css/bget.css?1744241634"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <link type="text/css" rel="stylesheet" href="/css/bgetm.css?1744241634" media="only screen and (max-width: 768px)"> <style>.kcfd{display:none;}</style> <script> <!-- var getElementsByClassName = document.getElementsByClassName ? function (cl){ return document.getElementsByClassName(cl); } : function (cl){ var elms = []; var objs = document.getElementsByTagName('*'); for(var i=0;i<objs.length;i++){ var obj = objs[i]; if(obj.className == cl){ elms.push(obj); } } return elms; }; function toggleField(clk,cl,show,hide){ var objs = getElementsByClassName(cl); for(var i=0;i<objs.length;i++){ var obj = objs[i]; if(!obj.style.display||obj.style.display == 'none'){ obj.style.display = 'block'; clk.innerHTML = ' « '+hide; 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} } } function Link_XtrctSeq2(form) { var dna_from; var dna_to; var dna_len; var plus_up = Number(form.XtrctSeq_UP.value) ; var plus_down = Number(form.XtrctSeq_DOWN.value); var vector = Number(form.VECTOR.value); var org = form.ORG.value; var chr = form.CHR.value; var kid = form.KEGGID.value; var url; if (plus_up == 0 && plus_down == 0) { url = "/entry/-f+-n+n+" + kid; } else { if (vector == 1) { dna_from = Number(form.FROM.value) - plus_up; dna_to = Number(form.TO.value) + plus_down; } else { dna_from = Number(form.FROM.value) - plus_down; dna_to = Number(form.TO.value) + plus_up; } url = "/dbget-bin/cut_sequence_genes.pl?FROM=" + dna_from + "&TO=" + dna_to +"&VECTOR=" + vector + "&ORG=" + org; if (chr) url += "&CHR=" + chr; } //window.open( url, "_self" ); location.href = url; } function go_taxonomy(form,params){ for(var key in params){ if(form[key]){ form.setAttribute(key,params[key]); } else{ var obj = document.createElement('input'); obj.setAttribute('type','hidden'); obj.setAttribute('name',key); obj.setAttribute('value',params[key]); form.appendChild(obj); } } form.submit(); } window.onload=function(){window.focus();init();}; //---> </script> </head> <body> <div> <table border=0 cellpadding=0 cellspacing=0><tr><td> <table border=0 cellpadding=0 cellspacing=0 width="683"><tr><td width=70><a href="/kegg/kegg2.html"><img align="middle" alt="KEGG" border=0 src="/Fig/bget/kegg2.gif"></a></td><td> </td><td><a name="enzyme:4.2.1.168"></a><font class="title2">ENZYME: 4.2.1.168</font></td><td class="tar vbot"><button class="btn" onclick="javascript:void(window.open('/kegg/document/help_bget_enzyme.html','KEGG_Help','toolbar=no,location=no,directories=no,width=720,height=640,resizable=yes,scrollbars=yes'));return false;">Help</button></td></tr></table><form method="post" action="/kegg-bin/search_htext" enctype="application/x-www-form-urlencoded" id="form1" name="form1"></form><table class="w1" width="650"> <tr> <td class="fr2 w1"> <table width="650" class="w2"> <tr><th class="th20 deft tal vmid"><span class="nowrap">Entry</span></th> <td class="td20 defd"><table class="w1" width="100%"><tr><td class="tal pd0"><code><span class="nowrap">EC 4.2.1.168 Enzyme <br> </span></code></td></tr></table></td></tr> <tr><th class="th21 deft tal vtop"><span class="nowrap">Name</span></th> <td class="td21 defd"><div class="cel"><div class="cel">GDP-4-dehydro-6-deoxy-alpha-D-mannose 3-dehydratase;<br> colD (gene name)<br> </div></div></td></tr> <tr><th class="th20 deft tal vtop"><span class="nowrap">Class</span></th> <td class="td20 defd"><div class="cel">Lyases;<br> Carbon-oxygen lyases;<br> Hydro-lyases<br> <button class="btn" onclick="location.href='/brite/ko01000+4.2.1.168';return false;">BRITE hierarchy</button></div></td></tr> <tr><th class="th21 deft tal vtop"><span class="nowrap">Sysname</span></th> <td class="td21 defd"><div class="cel">GDP-4-dehydro-alpha-D-rhamnose 3-hydro-lyase<br> </div></td></tr> <tr><th class="th20 deft tal vtop"><span class="nowrap">Reaction(IUBMB)</span></th> <td class="td20 defd"><div class="cel">GDP-4-dehydro-alpha-D-rhamnose + L-glutamate = GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose + 2-oxoglutarate + NH3 (overall reaction) [RN:<a href="/entry/R11409">R11409</a>];<br> (1a) GDP-4-dehydro-alpha-D-rhamnose + L-glutamate = 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol] + 2-oxoglutarate + H2O;<br> (1b) 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol] = 2-GDP-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] (spontaneous);<br> (1c) GDP-2-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] + H2O = GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose + NH3 (spontaneous)<br> </div></td></tr> <tr><th class="th21 deft tal vtop"><span class="nowrap">Reaction(KEGG)</span></th> <td class="td21 defd"><div class="cel"><a href="/entry/R11409">R11409</a><br> <button class="btn" onclick="location.href='/entry/R11409';return false;">Reaction</button></div></td></tr> <tr><th class="th20 deft tal vtop"><span class="nowrap">Substrate</span></th> <td class="td20 defd"><div class="cel">GDP-4-dehydro-alpha-D-rhamnose [CPD:<a href="/entry/C01222">C01222</a>];<br> L-glutamate [CPD:<a href="/entry/C00025">C00025</a>];<br> 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol];<br> GDP-2-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol];<br> H2O [CPD:<a href="/entry/C00001">C00001</a>]<br> </div></td></tr> <tr><th class="th21 deft tal vtop"><span class="nowrap">Product</span></th> <td class="td21 defd"><div class="cel"><div class="cel">GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose [CPD:<a href="/entry/C20612">C20612</a>];<br> 2-oxoglutarate [CPD:<a href="/entry/C00026">C00026</a>];<br> NH3 [CPD:<a href="/entry/C00014">C00014</a>];<br> 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol];<br> H2O [CPD:<a href="/entry/C00001">C00001</a>];<br> 2-GDP-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] (spontaneous)<br> </div></div></td></tr> <tr><th class="th20 deft tal vtop"><span class="nowrap">Comment</span></th> <td class="td20 defd"><div class="cel">This enzyme, involved in beta-L-colitose biosynthesis, is a unique vitamin-B6-dependent enzyme. In the first step of catalysis, the bound pyridoxal phosphate (PLP) cafactor is transaminated to the pyridoxamine 5'-phosphate (PMP) form of vitamin B6, using L-glutamate as the amino group donor. The PMP cofactor then forms a Schiff base with the sugar substrate and the resulting adduct undergoes a 1,4-dehydration to eliminate the 3-OH group. Hydrolysis of the product from the enzyme restores the PLP cofactor and results in the release of an unstable enamine intermediate. This intermediate tautomerizes to form an imine form, which hydrolyses spontaneously, releasing ammonia and forming the final product.<br> </div></td></tr> <tr><th class="th21 deft tal vtop"><span class="nowrap">History</span></th> <td class="td21 defd"><div class="cel">EC 4.2.1.168 created 2016<br> </div></td></tr> <tr><th class="th20 deft tal vtop"><span class="nowrap">Pathway</span></th> <td class="td20 defd"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><a href="/pathway/ec00541+4.2.1.168">ec00541</a> </span></td><td>Biosynthesis of various nucleotide sugars</td></tr></table><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><a href="/pathway/ec01100+4.2.1.168">ec01100</a> </span></td><td>Metabolic pathways</td></tr></table></td></tr> <tr><th class="th21 deft tal vtop"><span class="nowrap">Orthology</span></th> <td class="td21 defd"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><a href="/entry/K21131">K21131</a> </span></td><td>GDP-4-dehydro-6-deoxy-alpha-D-mannose 3-dehydratase</td></tr></table></td></tr> <tr><th class="th20 deft tal vtop"><span class="nowrap">Genes</span></th> <td class="td20 defd"><style>span.g1a{color:#003399}span.g1a:hover{color:#33cc99;cursor:pointer;}div.g1{display:none;}</style><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g11">EOI</span>: </span></td><td id="g11d">ECO111_2760(wbdK)</td></tr></table><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g12">EOK</span>: </span></td><td id="g12d">G2583_2551(wbdK)</td></tr></table><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g13">ELR</span>: </span></td><td id="g13d">ECO55CA74_12270</td></tr></table><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g14">YSI</span>: </span></td><td id="g14d">BF17_13445</td></tr></table><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g15">YAS</span>: </span></td><td id="g15d">N0H69_17375</td></tr></table><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g16">AAPC</span>: </span></td><td id="g16d">QG404_01580</td></tr></table><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g17">VGI</span>: </span></td><td id="g17d">MID13_00925</td></tr></table><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g18">SPSH</span>: </span></td><td id="g18d">FM037_09965</td></tr></table><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g19">CPS</span>: </span></td><td id="g19d">CPS_4201</td></tr></table><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g110">PTD</span>: </span></td><td id="g110d">PTET_a0496</td></tr></table><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g111">PSHO</span>: </span></td><td id="g111d">KQ246_01880</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g112">MOZ</span>: </span></td><td id="g112d">MoryE10_16090</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g113">ADJ</span>: </span></td><td id="g113d">ACIU1J_15920</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g114">RHOI</span>: </span></td><td id="g114d">PSR62_06905</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g115">RML</span>: </span></td><td id="g115d">FF011L_51340(arnB)</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g116">MSIL</span>: </span></td><td id="g116d">METEAL_02510</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g117">MAQI</span>: </span></td><td id="g117d">LDL77_09085</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g118">FBQ</span>: </span></td><td id="g118d">D1817_12920</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g119">NVA</span>: </span></td><td id="g119d">G3M78_07670</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g120">PAUN</span>: </span></td><td id="g120d">MJA45_22840</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g121">CASP</span>: </span></td><td id="g121d">NQ535_24820</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g122">ECLF</span>: </span></td><td id="g122d">QMP25_33390</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g123">IFN</span>: </span></td><td id="g123d">GM661_06815</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g124">HPRF</span>: </span></td><td id="g124d">HLPR_26900</td></tr></table></div><div class="g1"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap"><span class="g1a" id="g125">PFLU</span>: </span></td><td id="g125d">BWO91_13105</td></tr></table></div><a href="javascript:void(0)" onclick="javascript:toggleField(this,"g1","show all","hide")"> » show all</a><br> <script>for(var i=1;i<=25;i++){if(document.getElementById('g1'+i)){document.getElementById('g1'+i).onclick = function(e){geg1(this,e);};}}function geg1(bobj){var id = bobj.id;var ab = document.getElementById(id).innerText;var dt = document.getElementById(id+'d');var st = dt.innerText.replace(/\([^\)]+\)/g,'').replace(/ /g,'+');var gt = '/entry/'+ab+'+'+st;location.href = gt;}</script><input type="hidden" name="query" form="form1" value="EOI EOK ELR YSI YAS AAPC VGI SPSH CPS PTD PSHO MOZ ADJ RHOI RML MSIL MAQI FBQ NVA PAUN CASP ECLF IFN HPRF PFLU"><input type="hidden" name="htext" form="form1" value="br08601.keg"><input type="hidden" name="option" form="form1" value="-a"><button class="btn" onclick="javascript:go_taxonomy(document.form1,{"action":"/kegg-bin/search_htext"});return false;">Taxonomy</button></td></tr> <tr><th class="th21 deft tal vtop"><span class="nowrap">Reference</span></th> <td class="td21 defd"><div class="cel">1 [PMID:<a href="https://www.ncbi.nlm.nih.gov/pubmed/15610039">15610039</a>]</div></td></tr> <tr><th class="th20 rept tal vtop"><span class="nowrap"> Authors</span></th> <td class="td20 repd"><div class="cel">Alam J, Beyer N, Liu HW</div></td></tr> <tr><th class="th21 rept tal vtop"><span class="nowrap"> Title</span></th> <td class="td21 repd"><div class="cel">Biosynthesis of colitose: expression, purification, and mechanistic characterization of GDP-4-keto-6-deoxy-D-mannose-3-dehydrase (ColD) and GDP-L-colitose synthase (ColC).</div></td></tr> <tr><th class="th20 rept tal vtop"><span class="nowrap"> Journal</span></th> <td class="td20 repd"><div class="cel">Biochemistry 43:16450-60 (2004)<br>DOI:<a href="https://doi.org/10.1021/bi0483763">10.1021/bi0483763</a></div></td></tr> <tr><th class="th21 rept tal vtop"><span class="nowrap"> Sequence</span></th> <td class="td21 repd"><div class="cel">[ag:<a href="/entry/ag:AEP25496">AEP25496</a>]</div></td></tr> <tr><th class="th20 deft tal vtop"><span class="nowrap">Reference</span></th> <td class="td20 defd"><div class="cel">2 [PMID:<a href="https://www.ncbi.nlm.nih.gov/pubmed/17997582">17997582</a>]</div></td></tr> <tr><th class="th21 rept tal vtop"><span class="nowrap"> Authors</span></th> <td class="td21 repd"><div class="cel">Cook PD, Holden HM</div></td></tr> <tr><th class="th20 rept tal vtop"><span class="nowrap"> Title</span></th> <td class="td20 repd"><div class="cel">A structural study of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: caught in the act of geminal diamine formation.</div></td></tr> <tr><th class="th21 rept tal vtop"><span class="nowrap"> Journal</span></th> <td class="td21 repd"><div class="cel">Biochemistry 46:14215-24 (2007)<br>DOI:<a href="https://doi.org/10.1021/bi701686s">10.1021/bi701686s</a></div></td></tr> <tr><th class="th20 rept tal vtop"><span class="nowrap"> Sequence</span></th> <td class="td20 repd"><div class="cel">[eok:<a href="/entry/eok:G2583_2551">G2583_2551</a>]</div></td></tr> <tr><th class="th21 deft tal vtop"><span class="nowrap">Other DBs</span></th> <td class="td21 defd"><table class="w1"><tr><td class="vtop pd0"><span class="nowrap">ExplorEnz - The Enzyme Database: </span></td><td><a href="https://www.enzyme-database.org/query.php?ec=4.2.1.168">4.2.1.168</a></td></tr></table><table class="w1"><tr><td class="vtop pd0"><span class="nowrap">IUBMB Enzyme Nomenclature: </span></td><td><a href="https://iubmb.qmul.ac.uk/enzyme/EC4/2/1/168.html">4.2.1.168</a></td></tr></table><table class="w1"><tr><td class="vtop pd0"><span class="nowrap">ExPASy - ENZYME nomenclature database: </span></td><td><a href="https://enzyme.expasy.org/EC/4.2.1.168">4.2.1.168</a></td></tr></table><table class="w1"><tr><td class="vtop pd0"><span class="nowrap">BRENDA, the Enzyme Database: </span></td><td><a href="https://www.brenda-enzymes.info/enzyme.php?ecno=4.2.1.168">4.2.1.168</a></td></tr></table></td></tr> <tr><th class="th20 deft tal vmid"><span class="nowrap">LinkDB</span></th> <td class="td20 defd"><button class="btn" onclick="location.href='https://www.genome.jp/dbget-bin/get_linkdb?enzyme+4.2.1.168';return false;">All DBs</button></td></tr> </table></td></tr></table> <br></td></tr></table> <a href="/dbget/">DBGET</a> integrated database retrieval system</div> </body> </html>