Dihydrodipicolinate synthase: Difference between revisions

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Alexander Berchansky, Michal Harel

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-[[Image:2v9d.jpg|left|200px]]
+<StructureSection load='2v9d' size='350' side='right' caption='Structure of Se-Met dihydrodipicolinate synthase (PDB entry [[2v9d]])' scene=''>
-<!--
-The line below this paragraph, containing "STRUCTURE_2v9d", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2v9d|  PDB=2v9d  |  SIZE=350 | SCENE=2v9d/Spectrum_cartoon/4  }}
 '''CRYSTAL STRUCTURE OF YAGE, A PROPHAGE PROTEIN BELONGING TO THE DIHYDRODIPICOLINIC ACID SYNTHASE FAMILY FROM ''E. COLI K12'''''<br />
-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}}
-<applet load='V9da1.pdb' size='500' frame='true' align='right' scene='2v9d/Tetramer/1' />
 Cartoon representation of YagE <scene name='2v9d/Tetramer/5'>tetramer</scene> showing the 2-fold symmetry axes between monomers. Chains <font color='cyan'><b>A</b></font>, <font color='lime'><b>B</b></font>, <font color='magenta'><b>C</b></font>, and <font color='black'><b>D</b></font> are colored <font color='cyan'><b>cyan</b></font>, <font color='lime'><b>lime</b></font>, <font color='magenta'><b>magenta</b></font>, and <font color='black'><b>yellow</b></font>, respectively. <scene name='2v9d/Alignment/7'>Superposition</scene> of YagE <scene name='2v9d/Monomer/2'>monomer</scene> <font color='cyan'><b>(cyan)</b></font> with <scene name='2v9d/Alignment/8'>EcNAL</scene> ([[1nal]], <font color='black'><b>yellow</b></font>), <scene name='2v9d/Alignment/9'>SsKDGA</scene> ([[1w3i]], <font color='magenta'><b>magenta</b></font>), <scene name='2v9d/Alignment/10'>EcDHDSP</scene> ([[1xky]], <font color='lime'><b>lime</b></font>), and <scene name='2v9d/Alignment/11'>BaDHDPS</scene> ([[2ats]], <font color='blue'><b>blue</b></font>) monomers.
@@ Line 22: / Line 12: @@
 Members of the NAL protein subfamily have very similar active sites and a single amino acid substitution can significantly change their function. For example, NAL ([[1nal]]) gets DHDPS activity by substitution of a <scene name='2v9d/Leucine142/2'>leucine</scene> <font color='orange'><b>(orange)</b></font> to <scene name='2v9d/Arginine142/2'>arginine</scene> <font color='blue'><b>(blue)</b></font> at position 142. The possible active site region of <font color='cyan'><b>YagE</b></font> demonstrates closest sequence similarity to the active site of <font color='magenta'><b>KDG aldolase of SsKDGA</b></font> ([[1w3i]]) and <font color='black'><b>NAL of EcNAL</b></font> ([[1nal]]) (yellow), suggesting that this protein can perform either of these functions. Although the active site of EcDHDPS ([[1xky]]) and BaDHDPS ([[2ats]]) shows similarities, the important residue that differentiates between NAL and DHDPS, namely Leu142 (in [[1nal]]), is also present in YagE <scene name='2v9d/Leucine150/2'>(Leu150)</scene> <font color='cyan'><b>(labeled cyan)</b></font> at that particular position suggesting that YagE performs a NAL-related function rather than DHDPS-related one. In conclusion, the high-resolution X-ray structure of YagE provides a clue that it probably belongs to the NAL subfamily of proteins. Although the exact molecular function of YagE is still unknown, its structure provides a handle for understanding its molecular function based on knowledge about conserved residues of the putative active site.
 {{Clear}}
+</StructureSection>
+==3D structures of dihydrodipicolinate synthase==
+Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
+{{#tree:id=OrganizedByTopic|openlevels=0|
+*Dihydrodipicolinate synthase or 4-hydroxy-tetrahydrodipicolinate synthase
+**[[4dpp]], [[6vvi]] – AtDPS – ''Arabidopsis thaliana''<br />
+**[[3tuu]] – grDPS – grapevine<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 />
+**[[3pb0]], [[3pb2]] – TmDPS (mutant)<br />
+**[[1xky]], [[1xl9]] – BaDPS – ''Bacillus anthracis''<br />
+**[[1xxx]] – MtDPS – ''Mycobacterium tuberculosis''<br />
+**[[3l21]] – MtDPS (mutant)<br />
+**[[2hmc]], [[2r8w]], [[3b4u]], [[4i7u]], [[4i7v]] – DPS – ''Agrobacterium tumdefaciens''<br />
+**[[2ehh]] – DPS – ''Aquifex aeolicus''<br />
+**[[2rfg]] – DPS – ''Hahella chejuensis''<br />
+**[[2yxg]] – DPS – ''Methanocaldococcus jannaschii''<br />
+**[[3d0c]] – DPS – ''Oceanobacillus iheyensis''<br />
+**[[3daq]], [[3di0]] – SaDPS – ''Staphylococcus aureus''<br />
+**[[3dz1]] – DPS – ''Rhodopseudomonas palustris''<br />
+**[[3e96]] – DPS – ''Bacillus clausii''<br />
+**[[3cpr]] – DPS – ''Corynebacterium glutamicum''<br />
+**[[3g0s]] – DPS – ''Salmonella typhimurium''<br />
+**[[3flu]] – DPS – ''Neisseria meningitides''<br />
+**[[3ird]], [[3a5f]] – DPS – ''Clostridium botulinum''<br />
+**[[3vfl]] – SpDPS – ''Streptococcus pneumoniae''<br />
+**[[3ler]], [[3m5v]] – DPS – ''Campylobacter jejuni''<br />
+**[[3noe]], [[3ps7]], [[3qze]] – PaDPS – ''Psuedomonas aeruginosa''<br />
+**[[6p90]] - PaDPS (mutant) <br />
+**[[3pud]], [[3pul]], [[4dxv]] – AbDPS – ''Acinetobacter baumannii''<br />
+**[[3si9]] – DSP – ''Bartonella henselae''<br />
+**[[4icn]] - SbDPS – ''Shewanella benthica''<br />
+**[[4xky]] - DPS – ''Bacterioides thetaiotaomicron''<br />
+**[[5czj]] - SmDPS – ''Sinorhizobium meliloti''<br />
+**[[5ui3]] - DPS – ''Chlamydomonas reinhardtii''<br />
+**[[7loy]] - ClDPS – ''Candidatus liberibacter''<br />
+**[[6ue0]] - DPS – ''Klebsiella pneumoniae''<br />
+**[[5ktl]] - DPS – ''Trichormus variabilis''<br />
+**[[4r53]] - CjDPS – ''Campylobacter jejuni''<br />
+*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 />
+**[[3pue]] - AbDPS + Lys<br />
+**[[3tce]] - AbDPS + hydroxylysine<br />
+**[[3tdf]] - AbDPS + ketobutanoic acid<br />
+**[[3u8g]] - AbDPS + oxalic acid<br />
+**[[3uqn]] - AbDPS + oxamic acid<br />
+**[[3rk8]], [[3tak]] - AbDPS + pyruvate<br />
+**[[3puo]] - PaDPS + Lys<br />
+**[[3s8h]] - PaDPS + hydroxypropanoic acid<br />
+**[[4fha]] - SpDPS + Lys<br />
+**[[2vc6]] – SmDPS + pyruvate <br />
+**[[4ly8]], [[4mlj]], [[7kwn]], [[7l4b]] - CjDPS + 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]], [[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 />
-==About this Structure==
+*DHDPS ternary complexes
-V9D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V9D OCA].
+**[[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==
 Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12., Manicka S, Peleg Y, Unger T, Albeck S, Dym O, Greenblatt HM, Bourenkov G, Lamzin V, Krishnaswamy S, Sussman JL, Proteins. 2008 Jun;71(4):2102-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18361457 18361457 ]
+*Created with the participation of [[User:Jaime Prilusky|Jaime Prilusky]] and [[User:Michal Harel|Michal Harel]].
+[[Category:Topic Page]]
 [[Category: Escherichia coli]]
 [[Category: Single protein]]

Dihydrodipicolinate synthase: Difference between revisions

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