3axb | pdb_00003axb

Structure of a dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon, Aeropyrum pernix

spinqualitylabelsall models 3axb, resolution 1.92Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3axb is a 1 chain structure with sequence from Aeropyrum pernix. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: EDO, FAD, PRO NonStd Res: MSE Resources: FirstGlance, OCA, RCSB, PDBsum Publication Abstract from PubMed Two types of dye-linked l-proline dehydrogenase (PDH1, alpha4beta4-type hetero-octamer, and PDH2, alphabetagammadelta-type heterotetramer) have been identified so far in hyperthermophilic archaea. Here, we report the crystal structure of a third type of l-proline dehydrogenase, found in the aerobic hyperthermophilic archaeon Aeropyrum pernix, whose structure (homodimer) is much simpler than those of previously studied l-proline dehydrogenases. The structure was determined at a resolution of 1.92 A. The asymmetric unit contained one subunit, and a crystallographic 2-fold axis generated the functional dimer. The overall fold of the subunit showed similarity to that of the PDH1 beta-subunit, which is responsible for catalyzing l-proline dehydrogenation. However, the situation at the subunit-subunit interface of the A. pernix enzyme was totally different from that in PDH1. The presence of additional surface elements in the A. pernix enzyme contributes to a unique dimer association. Moreover, the C-terminal Leu(428), which is provided by a tail extending from the FAD-binding domain, shielded the active site, and an l-proline molecule was entrapped within the active site cavity. The K(m) value of a Leu(428) deletion mutant for l-proline was about 800 times larger than the K(m) value of the wild-type enzyme, although the k(cat) values did not differ much between the two enzymes. This suggests the C-terminal Leu(428) is not directly involved in catalysis, but it is essential for maintaining a high affinity for the substrate. This is the first description of an LPDH structure with l-proline bound, and it provides new insight into the substrate binding of LPDH. Crystal Structure of Novel Dye-linked L-Proline Dehydrogenase from Hyperthermophilic Archaeon Aeropyrum pernix.,Sakuraba H, Satomura T, Kawakami R, Kim K, Hara Y, Yoneda K, Ohshima T J Biol Chem. 2012 Jun 8;287(24):20070-80. Epub 2012 Apr 16. PMID:22511758 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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