Dihydrodipicolinate synthase: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Alexander Berchansky, Michal Harel

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-One approach of the incorporation of genetic material from different species into bacterial genomes is infection by a bacteriophage. The ''yagE'' gene is located in the ''E. coli K12'' genome and it is part of prophage ''CP4-6'' encoding a 33-kDa putative dihydrodipicolinate synthase (DHDPS)-like protein (UniProtKB/Swiss-prot: [http://www.expasy.org/uniprot/P75682 P75682]). This DHDPS-like domain is a member of the N-acetyl neuraminate lyase (NAL) subfamily comprises an 8-fold <scene name='2v9d/Alpha_beta/2'>α/β-barrel</scene> ([http://en.wikipedia.org/wiki/TIM_barrel TIM barrel]) with a small C-terminal α-helical domain (Inter pro: [http://www.ebi.ac.uk/interpro/ISearch?query=IPR005263 IPR005263]). Many enzymes possess this DHDPS domain (''e.g.'' HBPHA, KDGA, NAL, DOGDH, and DHDPS). All these enzymes contain an 8-fold α/β barrel and a small C-terminal α-helical region. <scene name='2v8z/Comparison/2'>Comparison</scene> between <font color='red'><b>orthorhombic</b></font> ([[2v8z]]) and <font color='cyan'><b>monoclinic</b></font> ([[2v9d]]) crystal forms of YagE revealed striking similarity.
+One approach of the incorporation of genetic material from different species into bacterial genomes is infection by a bacteriophage. The ''yagE'' gene is located in the ''E. coli K12'' genome and it is part of prophage ''CP4-6'' encoding a 33-kDa putative '''dihydrodipicolinate synthase''' or  '''4-hydroxy-tetrahydrodihydrodipicolinate synthase''' (DHDPS)-like protein (UniProtKB/Swiss-prot: [http://www.expasy.org/uniprot/P75682 P75682]). This DHDPS-like domain is a member of the N-acetyl neuraminate lyase (NAL) subfamily comprises an 8-fold <scene name='2v9d/Alpha_beta/2'>α/β-barrel</scene> ([http://en.wikipedia.org/wiki/TIM_barrel TIM barrel]) with a small C-terminal α-helical domain (Inter pro: [http://www.ebi.ac.uk/interpro/ISearch?query=IPR005263 IPR005263]). Many enzymes possess this DHDPS domain (''e.g.'' HBPHA, KDGA, NAL, DOGDH, and DHDPS). All these enzymes contain an 8-fold α/β barrel and a small C-terminal α-helical region. <scene name='2v8z/Comparison/2'>Comparison</scene> between <font color='red'><b>orthorhombic</b></font> ([[2v8z]]) and <font color='cyan'><b>monoclinic</b></font> ([[2v9d]]) crystal forms of YagE revealed striking similarity.
 {{Clear}}
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 **[[4dpp]], [[6vvi]] – AtDPS – ''Arabidopsis thaliana''<br />
 **[[3tuu]] – grDPS – grapevine<br />
-**[[1dhp]], [[1s5t]], [[1s5v]], [[1s5w]], [[2a6l]], [[2a6n]], [[2ojp]], [[2pur]], [[3den]], [[3i7q]], [[3i7r]] – EcDPS (mutant) – ''Escherichia coli''<br />
+**[[1dhp]], [[1s5t]], [[1s5v]], [[1s5w]], [[2a6l]], [[2a6n]], [[2ojp]], [[2pur]], [[3den]], [[3i7q]], [[3i7r]], [[7jz7]] – EcDPS (mutant) – ''Escherichia coli''<br />
 **[[1yxc]] - EcDPS<br />
 **[[1o5k]] – TmDPS – ''Thermotoga maritima''<br />
@@ Line 47: / Line 47: @@
 **[[3pud]], [[3pul]], [[4dxv]] – AbDPS – ''Acinetobacter baumannii''<br />
 **[[3si9]] – DSP – ''Bartonella henselae''<br />
-**[[4icn]] - DPS – ''Shewanella benthica''<br />
+**[[4icn]] - SbDPS – ''Shewanella benthica''<br />
 **[[4xky]] - DPS – ''Bacterioides thetaiotaomicron''<br />
 **[[5czj]] - SmDPS – ''Sinorhizobium meliloti''<br />
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 **[[7loy]] - ClDPS – ''Candidatus liberibacter''<br />
 **[[6ue0]] - DPS – ''Klebsiella pneumoniae''<br />
+**[[5ktl]] - DPS – ''Trichormus variabilis''<br />
+**[[4r53]] - CjDPS – ''Campylobacter jejuni''<br />
-*DPS complexes
+*DHDPS binary  complexes
 **[[4dpq]] - AtDPS + S-Lys<br />
 **[[4i7w]], [[6vvh]] - AtDPS + Lys<br />
+**[[7mds]] - AtDPS + inhibitor<br />
 **[[4hnn]] - grDPS + Lys<br />
 **[[5ud6]] - DPS + Lys – red alga<br />
@@ Line 70: / Line 73: @@
 **[[4fha]] - SpDPS + Lys<br />
 **[[2vc6]] – SmDPS + pyruvate <br />
-**[[4mlj]] - CjDPS + pyruvate – ''Campylobacter jejuni''<br />
+**[[4ly8]], [[4mlj]], [[7kwn]], [[7l4b]] - CjDPS + pyruvate <br />
-**[[6tzu]], [[6u01]] - CjDPS (mutant) + pyruvate <br />
+**[[6tzu]], [[6u01]], [[7kel]], [[7kg5]], [[7klq]], [[7klt]], [[7kn2]], [[7ko1]], [[7koc]], [[7kr8]], [[7ku6]], [[7kx1]], [[7lbd]] - CjDPS (mutant) + pyruvate <br />
+**[[7m06]] - CjDPS (mutant) + Lys derivative<br />
+**[[5f1u]], [[5f1v]] - CjDPS + inhibitor<br />
 **[[4mlr]] - CjDPS + pyruvate + Lys<br />
 **[[3di1]] - SaDPS + pyruvate<br />
 **[[1yxd]], [[2ats]] – EcDPS + S-Lys<br />
 **[[3c0j]] - EcDPS + hydroxypyruvate<br />
-**[[3du0]] - EcDPS + pyruvate<br />
+**[[3du0]], [[7jzf]] - EcDPS + pyruvate<br />
 **[[3i7s]] - EcDPS (mutant) + pyruvate<br />
 **[[4eou]] - EcDPS + succinic semialdehyde<br />
+**[[6nva]] - EcDPS + propionate<br />
+**[[5t25]], [[5t26]] - EcDPS + inhibitor<br />
 **[[3hij]] - BaDPS + pyruvate<br />
 **[[6xgs]] - DPS + citrate – ''Brucella suis''<br />
 **[[7lvl]] - ClDPS + S-Lys <br />
+**[[4nq1]] - DPS + pyruvate – ''Legionella pneumophila''<br />
+**[[6ue0]] - DPS + pyruvate – ''Klebsiella pneumoniae''<br />
+**[[5j5d]] - MtDPS + ketopimelic acid<br />
+*DHDPS ternary complexes
+**[[4pfm]] - SbDPS + Lys + pyruvate<br />
+**[[7kg2]] - CjDPS (mutant) + pyruvate + His<br />
+**[[7kxh]], [[7lcf]], [[7kwp]] – CjDPS + pyruvate + Lys derivative<br />
+**[[7kg9]], [[7kh4]], [[7kk1]], [[7kkd]], [[7kkg]], [[7kkt]], [[7kls]], [[7kly]], [[7km0]], [[7km1]], [[7kn9]], [[7knz]], [[7kpc]], [[7kpe]], [[7ko3]], [[7kr7]], [[7kto]], [[7kuz]], [[7kwf]], [[7kz2]] - CjDPS (mutant) + pyruvate + Lys derivative<br />
+**[[4m19]], [[4mlr]] - CjDPS + pyruvate + Lys<br />
+**[[7kxg]] - CjDPS + pyruvate + His<br />
+**[[7jzc]], [[7jzg]] - EcDPS (mutant) + Lys + pyruvate<br />
+**[[7jz9]], [[7jzb]] - EcDPS (mutant) + pyruvate + succinic semialdehyde <br />
+**[[7jza]] - EcDPS (mutant) + pyruvate + Lys + succinic semialdehyde <br />
+**[[7mjf]] - ClDPS + pyruvate + succinic semialdehyde <br />
 }}
 ==Reference==