3VQR

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

Summary for 3VQR

• Entry DOI: 10.2210/pdb3vqr/pdb
• Related: 3AXB
• Descriptor: Putative oxidoreductase, FLAVIN-ADENINE DINUCLEOTIDE, ACETATE ION, ... (5 entities in total)
• Functional Keywords: dinucleotide-binding fold, oxidoreductase
• Biological source: Aeropyrum pernix
• Total number of polymer chains: 2
• Total formula weight: 99623.87

Authors

Sakuraba, H.,Ohshima, T.,Satomura, T.,Yoneda, K. (deposition date: 2012-03-29, release date: 2012-04-25, Last modification date: 2023-11-08)

Primary citation

Sakuraba, H.,Satomura, T.,Kawakami, R.,Kim, K.,Hara, Y.,Yoneda, K.,Ohshima, T.
Crystal Structure of Novel Dye-linked L-Proline Dehydrogenase from Hyperthermophilic Archaeon Aeropyrum pernix
J.Biol.Chem., 287:20070-20080, 2012

PubMed Abstract: Two types of dye-linked L-proline dehydrogenase (PDH1, α4β4-type hetero-octamer, and PDH2, αβγδ-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 Å. 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 β-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.

PubMed: 22511758
DOI: 10.1074/jbc.M111.319038

Experimental method

X-RAY DIFFRACTION (2.01 Å)