The modular structure of alpha/beta-hydrolases: similarity of the N- and C-terminal domains to other proteins

DOI

To analyse the structural similarities of the N- and C-terminal domains, representative protein structures of each oxyanion hole type from the proteins of alpha/beta-hydrolase superfamilies 8 to 12 were selected from the Lipase Engineering Database (https://led.biocatnet.de/). The structures of the N- and C-terminal domains and the core domains were extracted and saved in separate .pdb files, which were then used to compare the domains by the "all against all" structure comparison tool on the Dali webserver (http://ekhidna2.biocenter.helsinki.fi/dali/). In a second step, the PDB (Protein Data Bank) search tool on the Dali server was used to compare the N- and C-terminal domains against all structures in PDB25, a subset resulting from clustering the whole PDB database with an identity threshold of 25%. The Dali server has different measures to determine similarity between proteins. The Z-Score is a measure for structural similarity, where a Z-score >2 implies significant structural similarities and thus a similar fold. Besides the Z-Score, the output also contains information about the root-mean-square deviation (rmsd) and the sequence identity.

Abbreviations: DPPIV: human dipeptidyl peptidase IV, APAP: acylaminoacyl peptidase from Aeropyrum pernix K1, RCE: Rhodococcus sp. MB1 cocaine esterase, HPL: human pancreatic lipase, PSML: Pseudomonas sp. MIS38 lipase, HEP: human epoxide hydrolase

Identifier
DOI https://doi.org/10.18419/darus-458
Related Identifier IsCitedBy https://doi.org/10.1111/febs.15071
Metadata Access https://darus.uni-stuttgart.de/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.18419/darus-458
Provenance
Creator Bauer, Tabea (ORCID: 0000-0002-1582-442X)
Publisher DaRUS
Contributor Pleiss, Jürgen
Publication Year 2019
Funding Reference Deutsche Forschungsgemeinschaft PL145/16-1 ; Deutsche Forschungsgemeinschaft EXC2075 ; Bundesministerium für Bildung und Forschung 031B0571A
Rights CC BY 4.0; info:eu-repo/semantics/openAccess; http://creativecommons.org/licenses/by/4.0
OpenAccess true
Contact Pleiss, Jürgen (Universität Stuttgart)
Representation
Resource Type hits from database search; Dataset
Format text/tab-separated-values; application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
Size 12221; 7161; 10216; 601; 2154; 2570; 50493
Version 1.0
Discipline Construction Engineering and Architecture; Engineering; Engineering Sciences; Life Sciences; Medicine