#!/usr/bin/perl -w
use strict;

my $protname;
my $rna;

while (<DATA>)  #while (<PROTEIN>) in your case
{
   if (/^VERSION/)
   {
      $protname  = (split)[1];
   }

   elsif (/^DBSOURCE/)
   {
      $rna = (split)[-1];
   }
}

print "protname = $protname\n";
print "rna = $rna\n";

__END__
PRINTS:
protname = YP_001648463.1
rna = NC_010202.1


__DATA__
LOCUS       YP_001648463             258 aa            linear   INV 17-JUN-2009
DEFINITION  cytochrome c oxidase subunit II [Ephydatia muelleri].
ACCESSION   YP_001648463
VERSION     YP_001648463.1  GI:164420795
DBLINK      Project: 28177
DBSOURCE    REFSEQ: accession NC_010202.1
KEYWORDS    .
....