Journal:Acta Cryst F:S2053230X21012632
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<b>Molecular Tour</b><br> | <b>Molecular Tour</b><br> | ||
| - | The high-resolution structure of a putative short-chain reductase from the commercially important bacteria ''Paraburkholderia xenovorans'' is reported (''Px''SDR). The reported apo structure of ''Px''SDR was determined in the monoclinic space group ''P''2<sub>1</sub> as a <scene name='89/899477/Cv/2'>prototypical SDR tetramer</scene>. ''P. xenovorans'' degrades organic wastes like polychlorinated biphenyls. ''Px''SDR shares less than 37% sequence identity with any known structure and assembles as a prototypical SDR tetramer. | + | The high-resolution structure of a putative short-chain reductase from the commercially important bacteria ''Paraburkholderia xenovorans'' is reported (''Px''SDR). The reported apo structure of ''Px''SDR was determined in the monoclinic space group ''P''2<sub>1</sub> as a <scene name='89/899477/Cv/2'>prototypical SDR tetramer</scene>. ''P. xenovorans'' degrades organic wastes like polychlorinated biphenyls. ''Px''SDR shares less than 37% sequence identity with any known structure (see static image below) and assembles as a prototypical SDR tetramer. |
| - | [[Image:Figure2t1.png|left| | + | [[Image:Figure2t1.png|left|450px|thumb|Structural and primary-sequence alignment of ''Px''SDR with the closest structures identified by ''PDBeFold''. Also shown is the percent identity matrix generated with ''Clustal''2.1. The structures are PDB entry [[5jc8]] (the apo structure of ''Px''SDR), PDB entry [[1iy8]] (the crystal structure of levodione reductase from ''Leifsonia aquatica''), PDB entry [[3ftp]] [3-ketoacyl-(acyl-carrier-protein) reductase from ''Burkholderia pseudomallei''], PDB entry [[6t6n]] [''Klebsiella pneumoniae'' FabG2(NADH-dependent) in complex with NADH] and PDB entry [[6ixm]] (ketone reductase ChKRED20 from the genome of ''Chryseobacterium''). The secondary-structure elements shown are α-helices (α), 3<sub>10</sub>-helices (η), β-strands (β) and β-turns (TT). Identical residues are shown in white on a red background and conserved residues are shown in red. This figure was generated using ''ESPript'' (Gouet et al., 1999, 2003)<ref name="Gouet1">PMID:10320398</ref>,<ref name="Gouet2">PMID:12824317</ref>.]] |
{{Clear}} | {{Clear}} | ||
| - | As expected, there is some conformational flexibility and differences between the substrate-binding cavity, which explains substrate specificity. Uniquely, the cofactor binding cavity of ''Px''SDR is not well conserved and differs from other SDRs. ''Px''SDR has an additional seven-amino acids that form an additional unique loop within the co-factor binding cavity. Further studies are required to determine how these differences affect the enzymatic functions of the SDR. This project is an educational collaboration between the Seattle Structural Genomics Center for Infectious Disease (SSGCID) and Hampton University where undergraduate students are engaged in structure-function analysis and publication of structures solved by the SSGCID. | + | As expected, there is some conformational flexibility and differences between the <scene name='89/899477/Cv/3'>substrate-binding cavity</scene>, which explains substrate specificity. The substrate-binding cavity is labeled in royalblue. The superposed structures are PDB entry [[5jc8]] (apo structure of ''Px''SDR, whitesmoke), PDB entry [[1iy8]] (crystal structure of levodione reductase from ''Leifsonia aquatica'', red), PDB entry [[3ftp]] [3-ketoacyl-(acyl-carrier-protein) reductase from ''Burkholderia pseudomallei'', yellow], PDB entry [[6t6n]] [''Klebsiella pneumoniae'' |
| + | FabG2(NADH-dependent) in complex with NADH, wheat] and PDB entry [[6ixm]] (ketone reductase ChKRED20 from the genome of ''Chryseobacterium'', aquamarine). The cofactor, NADH (magenta) and substrate, (4R)-2-methylpentane-2,4-diol (royalblue), are from PDB entry [[1iy8]]. Structures were superposed with ''PyMOL''. Uniquely, the <scene name='89/899477/Cv/4'>cofactor binding cavity</scene> of ''Px''SDR is not well conserved and differs from other SDRs. The cofactor-binding cavity is labeled in magenta. ''Px''SDR has an additional seven-amino acids that form an <scene name='89/899477/Cv/5'>additional unique loop</scene> within the co-factor binding cavity. Further studies are required to determine how these differences affect the enzymatic functions of the SDR. This project is an educational collaboration between the Seattle Structural Genomics Center for Infectious Disease (SSGCID) and Hampton University where undergraduate students are engaged in structure-function analysis and publication of structures solved by the SSGCID. | ||
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| + | '''PDB reference:''' putative short-chain reductase, [[5jc8]]. | ||
<b>References</b><br> | <b>References</b><br> | ||
Current revision
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![Structural and primary-sequence alignment of PxSDR with the closest structures identified by PDBeFold. Also shown is the percent identity matrix generated with Clustal2.1. The structures are PDB entry 5jc8 (the apo structure of PxSDR), PDB entry 1iy8 (the crystal structure of levodione reductase from Leifsonia aquatica), PDB entry 3ftp [3-ketoacyl-(acyl-carrier-protein) reductase from Burkholderia pseudomallei], PDB entry 6t6n [Klebsiella pneumoniae FabG2(NADH-dependent) in complex with NADH] and PDB entry 6ixm (ketone reductase ChKRED20 from the genome of Chryseobacterium). The secondary-structure elements shown are α-helices (α), 310-helices (η), β-strands (β) and β-turns (TT). Identical residues are shown in white on a red background and conserved residues are shown in red. This figure was generated using ESPript (Gouet et al., 1999, 2003),.](/wiki/index.php/Image:Figure2t1.png)
This page complements a publication in scientific journals and is one of the Proteopedia's Interactive 3D Complement pages. For aditional details please see I3DC.
