If I understand your problem, you want to convert

AB   AAAA_BBBBB             
DE   AC2-(EC 2.7.00.1) (Adaptor-associated
DE   protein 1).
//
[download]

into:

AB   AAAA_BBBBB             
DE   AC2-(EC 2.7.00.1) (Adaptor-associated protein 1).
[download]

(i.e, collapse all the lines beginning with the same "tag" for each "//" separated block).

if this is what you intend, try this script

#!/usr/bin/perl

use strict;
use warnings;

$/ = "//\n";
while (my $block = <DATA>){
  chomp $block;
  my @tags;  ## keep the order of the tags
  my %vals;
  foreach my $line (split /\n/, $block){
    $line =~ /(..)\s+(.+)$/;
    my ($tag,$val) = ($1,$2);
    if (!defined $vals{$tag}){
      push @tags,$tag;
      $vals{$tag}=$val;
    }else{
      $vals{$tag}.=" $val";
    }
  }
  for my $tag (@tags){
    print "$tag\t$vals{$tag}\n";
  }
  print "//\n";
}


__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]

Outputs:

AB      AAAA_BBBBB
DE      AC2-(EC 2.7.00.1) (Adaptor-associated protein 1).
//
ID      CCCCC_DDDDD
DE      Serine/threonine-protein kinase (EC 2.7.99.1) (Tyrosine bindin
+g protein) (p35BP).
PR      AAAAAAAAAAAAAAAAAAAAAAA.
//
ID      RRRRR_GGGGG
AC      Q6Q8;
DE      Serine/threonine-aaaaaa kinase (Tyrosine kinase 1) (Apoptosis-
+associated tyrosine kinase) (AATYK) (Brain binding protein) (p35BP).
PR      xxxxxxxxxxxxxx.
CD      zzzzzzzzzzzzzz.
//
[download]

Hope this helps!

citromatik