Maybe?

#! perl -slw
use strict;
$/ = '//';

while( <DATA> ) {
    s[(?:\A|\n)\S{2}\s*][ ]smg;
    s[^\s+][];
    print;
}
__DATA__
AB   AAAA_BBBBB
DE   AC2-(EC 2.7.00.1) (Adaptor-associated
DE   protein 1).
//
ID   CCCCC_DDDDD
DE   Serine/threonine-protein kinase (EC 2.7.99.1) (Tyrosine
DE   binding protein) (p35BP).
PR   AAAAAAAAAAAAAAAAAAAAAAA.
//
ID   RRRRR_GGGGG
AC   Q6Q8;
DE   Serine/threonine-aaaaaa kinase (Tyrosine
DE   kinase 1) (Apoptosis-associated tyrosine kinase) (AATYK) (Brain
DE   binding protein) (p35BP).
PR   xxxxxxxxxxxxxx.
CD   zzzzzzzzzzzzzz.
//
[download]

Gives

C:\test>junk
AAAA_BBBBB AC2-(EC 2.7.00.1) (Adaptor-associated protein 1).
CCCCC_DDDDD Serine/threonine-protein kinase (EC 2.7.99.1) (Tyrosine bi
+nding protein) (p35BP). AAAAAAAAAAAAAAAAAAAAAAA.
RRRRR_GGGGG Q6Q8; Serine/threonine-aaaaaa kinase (Tyrosine kinase 1) (
+Apoptosis-associated tyrosine kinase) (AATYK) (Brain binding protein)
+ (p35BP). xxxxxxxxxxxxxx. zzzzzzzzzzzzzz.
[download]