5DBU

Crystal structure of 2-deoxyribose-5-phosphate aldolase (1-220) from Streptococcus suis

Summary for 5DBU

• Entry DOI: 10.2210/pdb5dbu/pdb
• Related: 5DBT
• Descriptor: Deoxyribose-phosphate aldolase (2 entities in total)
• Functional Keywords: 2-deoxyribose-5-phosphate aldolase, streptococcus, lyase
• Biological source: Streptococcus suis GZ1
• Cellular location: Cytoplasm : D5AHU8
• Total number of polymer chains: 13
• Total formula weight: 302618.29

Authors

Cao, T.-P.,Choi, J.M.,Lee, S.H. (deposition date: 2015-08-22, release date: 2016-04-13, Last modification date: 2024-10-23)

Primary citation

Cao, T.-P.,Kim, J.-S.,Woo, M.-H.,Choi, J.M.,Jun, Y.,Lee, K.H.,Lee, S.H.
Structural insight for substrate tolerance to 2-deoxyribose-5-phosphate aldolase from the pathogen Streptococcus suis
J. Microbiol., 54:311-321, 2016

PubMed Abstract: 2-deoxyribose-5-phosphate aldolase (DERA) is a class I aldolase that catalyzes aldol condensation of two aldehydes in the active site, which is particularly germane in drug manufacture. Structural and biochemical studies have shown that the active site of DERA is typically loosely packed and displays broader substrate specificity despite sharing conserved folding architecture with other aldolases. The most distinctive structural feature of DERA compared to other aldolases is short and flexible C-terminal region. This region is also responsible for substrate recognition. Therefore, substrate tolerance may be related to the C-terminal structural features of DERA. Here, we determined the crystal structures of full length and C-terminal truncated DERA from Streptococcus suis (SsDERA). In common, both contained the typical (α/β)8 TIM-barrel fold of class I aldolases. Surprisingly, C-terminal truncation resulting in missing the last α9 and β8 secondary elements, allowed DERA to maintain activity comparable to the fulllength enzyme. Specifically, Arg186 and Ser205 residues at the C-terminus appeared mutually supplemental or less indispensible for substrate phosphate moiety recognition. Our results suggest that DERA might adopt a shorter C-terminal region than conventional aldolases during evolution pathway, resulting in a broader range of substrate tolerance through active site flexibility.

PubMed: 27033207
DOI: 10.1007/s12275-016-6029-4

Experimental method

X-RAY DIFFRACTION (2.797 Å)