Journal:Acta Cryst F:S2053230X21012632
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[[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), 33<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>.]] | [[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), 33<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 superposed |
| + | structures are PDB entry 5jc8 (apo structure of PxSDR, black), 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 and substrate, (4R)-2-methylpentane-2,4-diol, are from PDB entry 1iy8. Structures were superposed with PyMOL. 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. | ||
<b>References</b><br> | <b>References</b><br> | ||
Revision as of 13:33, 22 December 2021
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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), 3310-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)
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