The PDF header has the syntax of a comment. But, other than negligible comments it has a meaning. The header contains two numbers, the minor and the major version number, which refer to the specification upon which the file is built.
A reader should ignore features which are newer than the provided version and treat them as private data. Some readers such as Acrobat care about the file version but others just ignore them. In most cases the user doesn't notice but in some cases this can cause unexpected behavior. For example, if a file contains an OpenType font and its version number is 1.5 then the file is displayed correctly with the reader unaware of the version information but rejected by a version aware reader because the text refers to an "unknown" font type.
Therefore, a creator of a PDF file should choose the version numbers carefully since all features used within the file should conform to the corresponding specification. In general it is not a problem if the version number is higher than necessary.
However, if an updating tool, e.g. a digital signature tool, requires features which are newer than the version of the input file then it can update the version by adding an entry to the document's catalog dictionary. If such a version entry is present all objects of the updated file must conform to the new specification even if only a part of the objects have been updated.
The version update mechanism does not conflict with linearized files since they cannot have incremental updates. In this case the file can be rewritten using updated version numbers in the header.
In addition to the version numbers readers should identify any additional version information in the extensions entry in the document catalog.