Table 1

Results of the yeast-two hybrid interaction assays with PEX5

Yeast PEX5

Human PEX5


Species

Accession

Score*

Activity(Units/mg protein)

Standard deviation

Score*

Activity(Units/mg protein)

Standard deviation

Carboxyl terminus

Description


Canis familiaris

P81708

-

-

-

0.17

25

2

HCKGKDLSKYLASCNL

Lysozyme

Drosophila melanogaster

P13368

-

-

-

6.70

29

11

PLKDKQLYANEGVSRL

Sevenless protein

Gallus gallus

P00698

-

-

-

2.02

73

4

RCKGTDVQAWIRGCRL

Lysozyme

Rana nigromaculata

Q04604

-

-

-

0.13

91

15

LLMEAEDYQATYQSNL

Tyrosinase

Homo sapiens

P14679

-

-

-

4.01

242

10

LLMEKEDYHSLYQSHL

Tyrosinase

Bos taurus

P80209

-

-

-

7.04

310

58

FDRDQNRVGLAEAARL

Cathepsin D

Saccharomyces cerevisiae

P12687

2.72

482

37

-

-

-

KVEVIARSRRAFLSKL

Mitochondrial ribosomal protein L2, or MRP7

Synthetic construct

DHFR-SKL

11.51

195

45

-

-

-

EKGIKYKFEVYEKSKL

DHFR-SKL

Escherichia coli

P23893

4.81

270

26

11.35

473

57

DINNTIDAARRVFAKL

Glutamate-1-semialdehyde 2,1-aminomutase

E. coli

P78258

-9.46

164

31

5.59

566

70

FAVDQRKLEDLLAAKL

Transaldolase A

Methanopyrus kandleri

NP_613646

6.08

45

8

10.41

358

46

GMGRREGHPDVGPARL

Riboflavin synthase

Archaeoglobus fulgidus

NP_070998

7.57

206

19

-1.36

0

NA

EEVIRKIAEGLNKAKF

2-nitropropane dioxygenase


All eukaryotic target sequences (characterized by species, SWISS-PROT or NCBI-Refseq accession number, score from the PTS1 predictor [7], carboxy-terminal sequence and description) were tested for interaction with the tetratricopeptide (TPR) repeat domain of human PEX5, except for P12687 and DHFR-SKL where the corresponding TPR domains were derived from yeast PEX5. The prokaryotic proteins were assayed using PEX5 from both yeast and human. As the estimated length of the PTS1 signal is 12 carboxy-terminal residues [13], we chose the carboxy-terminal 16-mers to be sure that we have included the complete motif-carrying segment. *A PTS1 prediction score above zero is considered predictive of a functional PTS1 signal; a score between -10 and 0 is considered a 'twilight zone' prediction. It should be noted that the negative score for the DHFR-SKL carboxyl terminus in its context is generated by the PTS1 predictor [7] solely by terms that evaluate its potential accessibility for PEX5. A yeast-two hybrid assay is considered positive if the measured β-galactosidase activity is clearly greater than zero. Experience from previous test series suggests a lower limit of around 10 Miller Units per mg protein [12] for the detection of a productive interaction. The measured β-galactosidase activities (including standard deviations) range from weak (P81708, P13368) to strong (P80209, P12687).

Neuberger et al. Genome Biology 2004 5:R97   doi:10.1186/gb-2004-5-12-r97

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