You don't show us the code you have so it's a bit hard to give you concrete advice on how to change your code. I would approach the problem with something like the following code:

#!/usr/bin/perl -w
use strict;
my $last_tag = '';
my $buffer;
while (<DATA>) {
    if (! /^(..)\s+(.*)$/) { 
        warn "Malformed line >$_<";
        next;
    };
    my ($tag,$content) = ($1,$2);
   
    if ($tag ne $last_tag) {
        print "Collected: $tag, $buffer\n";
        $buffer = $content;
    } else {
        $buffer .= $content;
    };
};
__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.
//
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Please only put your code and data in between <code>..</code> tags.