Identification of Structural Domains in Proteins
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Identification of Structural Domains in Proteins. Marc A. Marti-Renom. Department of Biopharmaceutical Sciences University of California, San Francisco. Identification of Structural Domains in Proteins. Fragments. Marc A. Marti-Renom. Department of Biopharmaceutical Sciences

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Identification of Structural Domains in Proteins

Marc A. Marti-Renom

Department of Biopharmaceutical Sciences

University of California, San Francisco


Identification of Structural Domains in Proteins

Fragments

Marc A. Marti-Renom

Department of Biopharmaceutical Sciences

University of California, San Francisco


PAR-DOM

1phh (Oxydoreductase from Pseudomonas fluorescens)


Less significant

{1,2}{3,4}{4,5}

{5,6}{6,7}{7,8}{8,9}

Threshold #1,2Mammoth P-value

9

8

{1,2,3,4}

3

4

5

6

7

{6,7,8,9}

1

2

{5,6,7,8,9}

{3,4,5,6,7,8,9}

{all}

More significant

Lp

Up


9

8

3

4

5

6

7

1

2

{1,2,3,4}

{6,7,8,9}

{5,6,7,8,9}

{3,4,5,6,7,8,9}


9

8

3

4

5

6

7

1

2


9

8

3

4

5

6

7

1

2


9

8

3

4

5

6

7

1

2


9

8

3

4

5

6

7

1

2


9

8

3

4

5

6

7

1

2


9

8

3

4

5

6

7

1

2


9

8

3

4

5

6

7

1

2

Threshold #3 MCLCluster level (-I)

Stijn van Dongen (http://micans.org/mcl/)


Thresholds #1,2 MAMMOTH P-Value (Lp, Up)

High P-values  fewer partitions

Threshold #3 Cluster Level (-I)

Low –I cluster value  fewer partitions

Applied to the ~40,000 chains in PDB (Dec 2002)


Conservation

Residue number

1phh (Oxydoreductase from Pseudomonas fluorescens)


Conservation

Residue number

1phh (Oxydoreductase from Pseudomonas fluorescens)


Conservation

Residue number

1phh (Oxydoreductase from Pseudomonas fluorescens)


1phh (Oxydoreductase from Pseudomonas fluorescens)


ONE DOMAIN: (30)

1aak1tlk

1bbhA1ula

1bbpA1wsyA

1brd2ace

1fxiA2azaA

1gky2ccyA

1gmpA2gmfA

1gox2rn2

1ofv2stv

1pyp 2tmvP

1rbp3chy

1rcb3cla

1rveA3drf

1snc4blmA

1tie5p21

TWO DOMAINS: (20)

CodeAuthorsSCOP

------------------------------------------------------------------------------------------------------------------------------------

1ezm1-134 | 135-2981-153 | 154-298

1fnb19-161 | 162-314Not defined

1gpb19-489 | 490-841One domain

1lap1-150 | 171-4841-159 | 160-484

1pfkA0-138,251-301 | 139-250,302-319One domain

1ppn1-10,112-208 | 21-111,209-212One domain

1rhd1-158 | 159-2931-149 | 150-293

1sgt22-123,234,245 | 129,233One domain

1vsgA1-29,92-251 | 42-75,266-362One domain

1wsyB9-52,86-204 | 53-85,205-393Not defined

2cyp 3-145,266-294 | 164-265One domain

2had 1-155,230-310 | 156-229 One domain

3cd41-98 | 99-1781-97 | 98-178

3gapA1-129 | 139-208Not defined

3pgk1-185,403-415 | 200-392One domain

4gcr1-83 | 84-1741-85 | 86-174

5fbpA6-201 | 202-335One domain

8adh1-175,319-374 | 176-3181-174,325-374 | 175-324

8atcA1-137,288-310 | 144-2831-150 | 151-310

8atcB8-97 | 101-1528-100 | 101-153

THREE DOMAINS: (2)

CodeAuthorsSCOP

-------------------------------------------------------------------------------------------------------------------------------------

1phh 1-175 | 176-290 | 291-3941-173,276-394 | 174-275

3grs18-157,294-364 | 158-283 | 365-47818-165,291-363 | 166-290 | 364-478

FOUR DOMAINS: (3)

CodeAuthorsSCOP

-------------------------------------------------------------------------------------------------------------------------------------

1atnA 1-32,70-144,338-372 | 33-69 | 145-180,270-337 | 181-2691-146 | 147-375

3pmgA1-188 | 192-315 | 325-403 | 408-561Not defined

8acn2-200 | 201-317 | 320-513 | 538-7542-528 | 529-754

Islam et al. Prot. Eng. (1995)


Lp: 3-6, Up: 4-30, I: 1.2-5

ONE DOMAIN: (30)100%

1aak1tlk

1bbhA1ula

1bbpA1wsyA

1brd2ace

1fxiA2azaA

1gky2ccyA

1gmpA2gmfA

1gox2rn2

1ofv2stv

1pyp 2tmvP

1rbp3chy

1rcb3cla

1rveA3drf

1snc4blmA

1tie5p21

TWO DOMAINS: (20) 80%

CodeAuthorsResult

------------------------------------------------------------------------------------------------------------------------------------

1ezm1-134 | 135-29876.09%

1fnb19-161 | 162-31486.78%

1gpb19-489 | 490-84184.31%  3 domains

1lap1-150 | 171-48496.33%

1pfkA0-138,251-301 | 139-250,302-31997.80%

1ppn1-10,112-208 | 21-111,209-21293.53%

1rhd1-158 | 159-29399.32%

1sgt22-123,234,245 | 129,23387.34%

1vsgA1-29,92-251 | 42-75,266-36257.99%  3 domains

1wsyB9-52,86-204 | 53-85,205-39388.28%

2cyp 3-145,266-294 | 164-26587.91%

2had 1-155,230-310 | 156-229 93.20%

3cd41-98 | 99-178100.0%

3gapA1-129 | 139-20896.97%

3pgk1-185,403-415 | 200-39296.92%

4gcr1-83 | 84-174100.0%

5fbpA6-201 | 202-33594.83%

8adh1-175,319-374 | 176-31877.48%

8atcA1-137,288-310 | 144-28397.99%

8atcB8-97 | 101-152100.0%

THREE DOMAINS: (2) 50%

CodeAuthorsResult

-------------------------------------------------------------------------------------------------------------------------------------

1phh 1-175 | 176-290 | 291-39482.70%

3grs18-157,294-364 | 158-283 | 365-47898.22%

FOUR DOMAINS: (3) 67%

CodeAuthorsResult

-------------------------------------------------------------------------------------------------------------------------------------

1atnA 1-32,70-144,338-372 | 33-69 | 145-180,270-337 | 181-26973.85%  3 domains

3pmgA1-188 | 192-315 | 325-403 | 408-56193.75%

8acn2-200 | 201-317 | 320-513 | 538-75489.53%

OVERALL:

(49/55 OK) 89.1%

Definition:

OK if Same # dom.

> 85% correct


for single values, e.g. Lp=3, Up=8, I=1.5

ONE DOMAIN: (28)

1aak 1bbhA

1bbpA 1brd

1fxiA 1gky

1gmpA 1gox

1ofv 1pyp

1rbp 1rcb

1rveA 1snc

1tie 1tlk

1ula 1wsyA

2azaA 2ccyA

2rn2 2stv

2tmvP 3chy

3cla 3dfrA

4blmA 5p21

ONE DOMAIN: (30) 97%

1aak1tlk

1bbhA1ula

1bbpA1wsyA

1brd2ace

1fxiA2azaA

1gky2ccyA

1gmpA2gmfA

1gox2rn2

1ofv2stv

1pyp 2tmvP

1rbp3chy

1rcb3cla

1rveA3drf

1snc4blmA

1tie5p21

TWO DOMAINS: (20) 30%

CodeAuthorsResult

------------------------------------------------------------------------------------------------------------------------------------

1ezm1-134 | 135-29845.12%  1 domain

1fnb19-161 | 162-31451.53%  1 domain

1gpb19-489 | 490-84184.31%  3 domains

1lap1-150 | 171-48467.60%  1 domain

1pfkA0-138,251-301 | 139-250,302-31997.17%

1ppn1-10,112-208 | 21-111,209-21253.23%  1 domain

1rhd1-158 | 159-29397.95%

1sgt22-123,234,245 | 129,23345.41%  1 domain

1vsgA1-29,92-251 | 42-75,266-36239.50%

1wsyB9-52,86-204 | 53-85,205-39381.68%

2cyp 3-145,266-294 | 164-26587.91%

2had 1-155,230-310 | 156-229 76.05%  1 domain

3cd41-98 | 99-17898.87%

3gapA1-129 | 139-20865.15%  1 domain

3pgk1-185,403-415 | 200-39296.92%

4gcr1-83 | 84-17452.02%  1 domain

5fbpA6-201 | 202-33594.22%

8adh1-175,319-374 | 176-31861.39%  1 domain

8atcA1-137,288-310 | 144-28353.18%  1 domain

8atcB8-97 | 101-15263.83%  1 domain

THREE DOMAINS: (2) 50%

CodeAuthorsResult

-------------------------------------------------------------------------------------------------------------------------------------

1phh 1-175 | 176-290 | 291-39444.53%  1 domain

3grs18-157,294-364 | 158-283 | 365-47896.67%

FOUR DOMAINS: (3) 67%

CodeAuthorsResult

-------------------------------------------------------------------------------------------------------------------------------------

1atnA 1-32,70-144,338-372 | 33-69 | 145-180,270-337 | 181-26955.80%  2 domains

3pmgA1-188 | 192-315 | 325-403 | 408-56190.62%

8acn2-200 | 201-317 | 320-513 | 538-75489.39%

OVERALL:

(38/55 OK) 69.1%

Definition:

OK if Same # dom.

> 85% correct


Values Employed…


Results (for values based on length)

ONE DOMAIN: (28)

1aak 1bbhA

1bbpA 1brd

1fxiA 1gky

1gmpA 1gox

1ofv 1pyp

1rbp 1rcb

1rveA 1snc

1tie 1tlk

1ula 1wsyA

2azaA 2ccyA

2rn2 2stv

2tmvP 3chy

3cla 3dfrA

4blmA 5p21

ONE DOMAIN: (30) 97%

1aak1tlk

1bbhA1ula

1bbpA1wsyA

1brd2ace

1fxiA2azaA

1gky2ccyA

1gmpA2gmfA

1gox2rn2

1ofv2stv

1pyp 2tmvP

1rbp3chy

1rcb3cla

1rveA3drf

1snc4blmA

1tie5p21

TWO DOMAINS: (20) 60%

CodeAuthorsResult

------------------------------------------------------------------------------------------------------------------------------------

1ezm1-134 | 135-29845.12%  1 domain

1fnb19-161 | 162-31451.53%  1 domain

1gpb19-489 | 490-84182.00%  3 domains

1lap1-150 | 171-48467.60%  1 domain

1pfkA0-138,251-301 | 139-250,302-31996.23%

1ppn1-10,112-208 | 21-111,209-21290.55%

1rhd1-158 | 159-29397.95%

1sgt22-123,234,245 | 129,23386.46%

1vsgA1-29,92-251 | 42-75,266-36252.66%  3 domains

1wsyB9-52,86-204 | 53-85,205-39388.28%

2cyp 3-145,266-294 | 164-26587.91%

2had 1-155,230-310 | 156-229 76.05%  1 domain

3cd41-98 | 99-17898.87%

3gapA1-129 | 139-20874.24%

3pgk1-185,403-415 | 200-39296.92%

4gcr1-83 | 84-17495.95%

5fbpA6-201 | 202-33593.92%

8adh1-175,319-374 | 176-31873.19%

8atcA1-137,288-310 | 144-28396.99%

8atcB8-97 | 101-15297.87%

THREE DOMAINS: (2) 50%

CodeAuthorsResult

-------------------------------------------------------------------------------------------------------------------------------------

1phh 1-175 | 176-290 | 291-39444.53%  1 domain

3grs18-157,294-364 | 158-283 | 365-47893.78%

FOUR DOMAINS: (3) 67%

CodeAuthorsResult

-------------------------------------------------------------------------------------------------------------------------------------

1atnA 1-32,70-144,338-372 | 33-69 | 145-180,270-337 | 181-26973.32%  3 domains

3pmgA1-188 | 192-315 | 325-403 | 408-56190.62%

8acn2-200 | 201-317 | 320-513 | 538-75489.39%

OVERALL:

(44/55 OK) 80%

Definition:

OK if Same # dom.

> 85% correct


Authors

SCOP

PAR-DOM

1bbhA

1phh


Authors

SCOP

PAR-DOM

1gpb

1vsgA


Authors

SCOP

PAR-DOM

1gpb

1vsgA


1

477

1f3iA

Transposase 11

Transposase Tn5

PFam

Islam et al

PAR-DOM

Islam et al

PFam

PAR-DOM


Needs careful interpretation due to small dataset

Jones et al. Prot. Sci. (1998)


Needs careful interpretation due to small dataset

Jones et al. Prot. Sci. (1998)


Domains  Fragments


G-protein (1gotB) all-b 7 bladed beta propeller domain


1ee9A 17.9% id. 2.3Å

6timB 11.1% id. 2.6Å

Ribosomal protein S6 (1ris) a+b Ferrodoxin Like domain


Cytochrome C Peroxidase (2cyp) all-a  CCP-like domain

29/34 2.9Å

27/35 3.2Å


  • PAR-DOM

  • Domains  Fragments


Acknowledgments

Andrej Sali

David Katz

Angel Ortiz

Frank Alber

Fred Davis

Damien Devos

Narayanan Eswar

Dmitry Korkin

M. S. Madhusudhan

Ursula Pieper

Andrea Rossi

Min-yi Shen

Maya Topf

http://www.salilab.org


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