How can we extract entire Marketo Database?

Entire? No. The API docs show you what's accessible (of course not in native binary database form but in serialized CSV and/or JSON).

There are numerous data sources used by the platform that can't be extracted — this is the case, of course, with all proprietary SaaS platforms, and nearly all hosted platforms in general! An API, by definition, abstracts some of the internal workings of a platform using a standardized set of contracts. But you're not accessing the databases themselves.*

As the docs describe, you can bulk download activity logs using the Bulk Activity Log API, people using the Bulk Lead Extract API, and custom objects using the Bulk CO Extract API.

Several other structural components, like Programs and Tags, can also be extracted using the REST API, although those use paginated JSON endpoints (rather than all-at-once file downloads). And of course all the Asset types listed in the docs can be crawled as well. Yet you mustn't mistake all of this for "extracting the complete Marketo database(s)."

* the exception would be the database backup API itself, I suppose,

though even a database wire protocol like TDS is consuming an API