6OAD

2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str. K-12 substr. MG1655.

Summary for 6OAD

• Entry DOI: 10.2210/pdb6oad/pdb
• Descriptor: Peptidase B, ZINC ION, CALCIUM ION, ... (9 entities in total)
• Functional Keywords: structural genomics, center for structural genomics of infectious diseases, csgid, aminopeptidase b, hydrolase
• Biological source: Escherichia coli str. K-12 substr. MG1655
• Total number of polymer chains: 12
• Total formula weight: 564697.89

Authors

Minasov, G.,Shuvalova, L.,Wawrzak, Z.,Kiryukhina, O.,Grimshaw, S.,Kwon, K.,Satchell, K.J.F.,Center for Structural Genomics of Infectious Diseases (CSGID) (deposition date: 2019-03-15, release date: 2019-03-27, Last modification date: 2023-10-11)

Primary citation

Minasov, G.,Lam, M.R.,Rosas-Lemus, M.,Slawek, J.,Woinska, M.,Shabalin, I.G.,Shuvalova, L.,Palsson, B.O.,Godzik, A.,Minor, W.,Satchell, K.J.F.
Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis.
Protein Sci., 29:1618-1628, 2020

PubMed Abstract: Protein degradation by aminopeptidases is involved in bacterial responses to stress. Escherichia coli produces two metal-dependent M17 family leucine aminopeptidases (LAPs), aminopeptidase A (PepA) and aminopeptidase B (PepB). Several structures have been solved for PepA as well as other bacterial M17 peptidases. Herein, we report the first structures of a PepB M17 peptidase. The E. coli PepB protein structure was determined at a resolution of 2.05 and 2.6 Å. One structure has both Zn and Mn , while the second structure has two Zn ions bound to the active site. A 2.75 Å apo structure is also reported for PepB from Yersinia pestis. Both proteins form homohexamers, similar to the overall arrangement of PepA and other M17 peptidases. However, the divergent N-terminal domain in PepB is much larger resulting in a tertiary structure that is more expanded. Modeling of a dipeptide substrate into the C-terminal LAP domain reveals contacts that account for PepB to uniquely cleave after aspartate.

PubMed: 32306515
DOI: 10.1002/pro.3876

Experimental method

X-RAY DIFFRACTION (2.05 Å)