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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Marc a marti renom

Identification of Structural Domains in Proteins

Marc A. Marti-Renom

Department of Biopharmaceutical Sciences

University of California, San Francisco


Marc a marti renom

Identification of Structural Domains in Proteins

Fragments

Marc A. Marti-Renom

Department of Biopharmaceutical Sciences

University of California, San Francisco


Marc a marti renom

PAR-DOM

1phh (Oxydoreductase from Pseudomonas fluorescens)


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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


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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}


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9

8

3

4

5

6

7

1

2


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9

8

3

4

5

6

7

1

2


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9

8

3

4

5

6

7

1

2


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9

8

3

4

5

6

7

1

2


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9

8

3

4

5

6

7

1

2


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9

8

3

4

5

6

7

1

2


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9

8

3

4

5

6

7

1

2

Threshold #3 MCLCluster level (-I)

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


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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)


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Conservation

Residue number

1phh (Oxydoreductase from Pseudomonas fluorescens)


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Conservation

Residue number

1phh (Oxydoreductase from Pseudomonas fluorescens)


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Conservation

Residue number

1phh (Oxydoreductase from Pseudomonas fluorescens)


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1phh (Oxydoreductase from Pseudomonas fluorescens)


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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)


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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


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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


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Values Employed…


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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


Marc a marti renom

Authors

SCOP

PAR-DOM

1bbhA

1phh


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Authors

SCOP

PAR-DOM

1gpb

1vsgA


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Authors

SCOP

PAR-DOM

1gpb

1vsgA


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1

477

1f3iA

Transposase 11

Transposase Tn5

PFam

Islam et al

PAR-DOM

Islam et al

PFam

PAR-DOM


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Needs careful interpretation due to small dataset

Jones et al. Prot. Sci. (1998)


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Needs careful interpretation due to small dataset

Jones et al. Prot. Sci. (1998)


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Domains  Fragments


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


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1ee9A 17.9% id. 2.3Å

6timB 11.1% id. 2.6Å

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


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

29/34 2.9Å

27/35 3.2Å


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  • PAR-DOM

  • Domains  Fragments


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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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