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PDB-wide identification of physiological hetero-oligomeric assemblies based on conserved quaternary structure geometry.

ABSTRACT: An accurate understanding of biomolecular mechanisms and diseases requires information on protein quaternary structure (QS). A critical challenge in inferring QS information from crystallography data is distinguishing biological interfaces from fortuitous crystal-packing contacts. Here, we employ QS conservation across homologs to infer the biological relevance of hetero-oligomers. We compare the structures and compositions of hetero-oligomers, which allow us to annotate 7,810 complexes as physiologically relevant, 1,060 as likely errors, and 1,432 with comparative information on subunit stoichiometry and composition. Excluding immunoglobulins, these annotations encompass over 51% of hetero-oligomers in the PDB. We curate a dataset of 577 hetero-oligomeric complexes to benchmark these annotations, which reveals an accuracy >94%. When homology information is not available, we compare QS across repositories (PDB, PISA, and EPPIC) to derive confidence estimates. This work provides high-quality annotations along with a large benchmark dataset of hetero-assemblies.

SUBMITTER: Dey S

PROVIDER: S-EPMC8575123 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Many enzymes form homooligomers, yet the functional significance of self-association is seldom obvious. Herein, we examine the connection between oligomerization and catalytic function for proline utilization A (PutA) enzymes. PutAs are bifunctional enzymes that catalyze both reactions of proline catabolism. Type A PutAs are the smallest members of the family, possessing a minimal domain architecture consisting of N-terminal proline dehydrogenase and C-terminal l-glutamate-?-semialdehyde dehydrogenase modules. Type A PutAs form domain-swapped dimers, and in one case (Bradyrhizobium japonicum PutA), two of the dimers assemble into a ring-shaped tetramer. Whereas the dimer has a clear role in substrate channeling, the functional significance of the tetramer is unknown. To address this question, we performed structural studies of four-type A PutAs from two clades of the PutA tree. The crystal structure of Bdellovibrio bacteriovorus PutA covalently inactivated by N-propargylglycine revealed a fold and substrate-channeling tunnel similar to other PutAs. Small-angle X-ray scattering (SAXS) and analytical ultracentrifugation indicated that Bdellovibrio PutA is dimeric in solution, in contrast to the prediction from crystal packing of a stable tetrameric assembly. SAXS studies of two other type A PutAs from separate clades also suggested that the dimer predominates in solution. To assess whether the tetramer of B. japonicum PutA is necessary for catalytic function, a hot spot disruption mutant that cleanly produces dimeric protein was generated. The dimeric variant exhibited kinetic parameters similar to the wild-type enzyme. These results implicate the domain-swapped dimer as the core structural and functional unit of type A PutAs.Proline dehydrogenase (EC 1.5.5.2); l-glutamate-?-semialdehyde dehydrogenase (EC 1.2.1.88).The atomic coordinates and structure factor amplitudes have been deposited in the Protein Data Bank under accession number 5UR2. The SAXS data have been deposited in the SASBDB under the following accession codes: SASDCP3 (BbPutA), SASDCQ3 (DvPutA 1.5 mg·mL-1 ), SASDCX3 (DvPutA 3.0 mg·mL-1 ), SASDCY3 (DvPutA 4.5 mg·mL-1 ), SASDCR3 (LpPutA 3.0 mg·mL-1 ), SASDCV3 (LpPutA 5.0 mg·mL-1 ), SASDCW3 (LpPutA 8.0 mg·mL-1 ), SASDCS3 (BjPutA 2.3 mg·mL-1 ), SASDCT3 (BjPutA 4.7 mg·mL-1 ), SASDCU3 (BjPutA 7.0 mg·mL-1 ), SASDCZ3 (R51E 2.3 mg·mL-1 ), SASDC24 (R51E 4.7 mg·mL-1 ), SASDC34 (R51E 7.0 mg·mL-1 ).

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PDB-wide identification of physiological hetero-oligomeric assemblies based on conserved quaternary structure geometry.

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