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Phosphodiesterase

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[[2zo9]], [[2zoa]] – PDE + malonate – ''Enterobacter aerogenes''<BR />
[[2zo9]], [[2zoa]] – PDE + malonate – ''Enterobacter aerogenes''<BR />
[[3mz2]], [[3no3]] – PDE – ''Parabacterioides distasonia''<BR />
[[3mz2]], [[3no3]] – PDE – ''Parabacterioides distasonia''<BR />
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===C-di-GMP PDE===
 +
 +
See [[C-di-GMP phosphodiesterase]]
[[2ahd]] – PDE – ''Methanocaldococcus jannaschii''<BR />
[[2ahd]] – PDE – ''Methanocaldococcus jannaschii''<BR />

Revision as of 06:51, 27 August 2014

Template:STRUCTURE 3g45

Phosphodiesterase (PDE) breaks phosphodiesteric bonds in cyclic nucleotides like cAMP and cGMP PDE is a regulator of signal transduction. In mammals PDE is classified into 11 families.

  • Tyrosyl-DNA PDE hydrolizes phosphodiester bond at the 3’-end of DNA linked to a tyrosyl moiety.
  • Glycerophosphodiester PDE hydrolyzes various glycerophosphodiesters to release glycerol-3-phosphate and alcohol.

Specific phosphodiesterases are in C-di-GMP specific phosphodiesterases. See details on PDE 6 in User:Rick H. Cote/PDE6.

Contents

3D Structures of phosphodiesterase

Updated on 27-August-2014

cAMP PDE

1loi – rPDE N terminal – rat – NMR
3ib7 – MtPDE – Mycobacterium tuberculosis
3ib8 – MtPDE + AMP

cGMP PDE

1ksg, 1ksh, 1ksj – hPDE δ subunit + ARF-like protein - human
2ju4 - PDE γ subunit – bovine - NMR
4kie, 4lyk - EcPDE EAL domain – Escherichia coli
4lj3 - EcPDE EAL domain + GMP

PDE 1

1taz – hPDE 1b catalytic domain – human
2r8q - PDE 1b catalytic domain + inhibitor – Leishmania major
4i15 – PDE catalytic domain – Trypanosoma brucei

PDE 2

1f0j – mPDE 2a regulatory domain (mutant) – mouse
1z1l, 3ibj, 3itm - hPDE 2a catalytic domain
3itu, 4htx, 4htz, 4jib - hPDE 2a catalytic domain + inhibitor

PDE 3

1so2, 1soj – hPDE 3b catalytic domain + inhibitor

PDE 4a

3i8v, 3tvx – hPDE 4a catalytic domain + inhibitor

PDE 4b

1f0j – hPDE 4b catalytic domain (mutant)
1ro6, 1xmy, 1xn0 - hPDE 4b catalytic domain + anti-inflammatory drug
1xot - hPDE 4b catalytic domain + drug
1tb5, 1ro9, 1ror - hPDE 4b catalytic domain + AMP
1y2h, 1y2j, 2qyl, 3d3p, 3kkt, 3frg, 3gwt, 3ly2, 3hmv, 3o56, 3o57, 3o0j, 3w5e, 3wd9, 4myq - hPDE 4b catalytic domain + inhibitor
3g45 - hPDE 4b catalytic domain + modulator

PDE 4c

2qym – hPDE 4c catalytic domain

PDE 4d

1e9k - hPDE 4d5 N terminal – NMR
1mkd, 1oyn, 1q9m, 1tbb, 1xoq, 3g4k, 3g4l - hPDE 4d catalytic domain + anti-inflammatory drug
1xlx, 1xlz, 1xm4, 1xm6, 1xmu, 1xom, 1xon, 1xor, 1xos, 3iak - hPDE 4d catalytic domain + drug
1ptw, 1tb7 - hPDE 4d catalytic domain + AMP
2pw3 - hPDE 4d catalytic domain (mutant) + AMP
1y2b, 1y2c, 1y2d, 1y2e, 1y2k, 1zkn, 2fm0, 2fm5, 2qyn, 3k4s, 3sl3, 3sl4, 3sl5, 3sl6, 3sl8, 3v9b - hPDE 4d catalytic domain + inhibitor
3iad, 3g4g, 3g4i, 3g58 - hPDE 4d catalytic domain + modulator

PDE 5

2h40 - hPDE 5a catalytic domain
1t9r - hPDE 5 catalytic domain
2k31 - mPDE 5a cGMP-binding domain – NMR
3lfv, 3mf0, 2xss - hPDE 5a GAF domain
1rkp, 3tgg – hPDE 5a1 catalytic domain (mutant) + inhibitor
2chm, 3tse, 3tsf, 4g2w, 4g2y, 4i9z, 4ia0 - hPDE 5a catalytic domain + inhibitor
2h44, 3bjc, 3hc8, 3hdz, 3shy, 3shz, 3sie, 3tge - hPDE 5a1 catalytic domain + inhibitor
1udt, 1udu, 1uho, 1tbf, 1xoz, 1xp0, 2h42, 3b2r - hPDE 5 catalytic domain + drug
3jwq - hPDE 5/hPDE 6 catalytic domain + drug
3jwr - hPDE 5/hPDE 6 catalytic domain + hPDE γ subunit peptide + inhibitor
1t9s - hPDE 5 catalytic domain + GMP

PDE 6

3dba - PDE 6c cGMP-binding domain – chicken
3t5g – hPDE 6d δ subunit + GTP-binding protein RHEB
3t5i - hPDE 6d δ subunit + GTP-binding protein RHEB peptide
4jhp - hPDE 6d δ subunit + RPGR
4jv6, 4jv8, 4jvb, 4jvf - hPDE 6d δ subunit + inhibitor

PDE 7

1zkl, 3g3n – hPDE 7a catalytic domain + inhibitor

PDE 8

3ecm – hPDE 8a catalytic domain
3ecn – hPDE 8a catalytic domain + inhibitor

PDE 9

2hd1, 2yy2, 3jsi, 3jsw, 3k3e, 3k3h, 4e90, 4g2j, 4g2l, 4gh6 - hPDE 6d δ subunit + RPGR
3n3z, 3qi3, 3qi4 - hPDE 9a catalytic domain (mutant) + inhibitor
3dy8, 3dyl, 3dyn, 3dyq, 3dys - hPDE 9 catalytic domain + GMP
4gyz - mPDE 9 catalytic domain + AMP

PDE 10

2o8h – rPDE 10a catalytic domain
2oup - hPDE 10a catalytic domain
2zmf – hPDE 10a C terminal
2ous, 2ouv - hPDE 10a2 catalytic domain (mutant)
2ovv, 2ovy – rPDE 10a catalytic domain + inhibitor
2qyk, 3lxg, 2y0j, 3qpn, 3qpo, 3qpp, 3sn7, 3sni, 3snl, 3wi2, 4ael, 4ajd, 4ajf, 4ajg, 4ajm, 4ddl, 4fcb, 4fcd, 4heu, 4hf4, 4lkq, 4llj, 4llk, 4llp, 4llx, 4lm0, 4lm1, 4lm2, 4lm3, 4lm4, 4muw, 4mvh - hPDE 10a catalytic domain + inhibitor
2wey, 3hqw, 3hqy, 3hqz, 3hr1, 3ui7, 3uuo, 4bbx, 4dff - hPDE 10a catalytic domain + schizophrenia drug
2oun - hPDE 10a2 catalytic domain + AMP
2our, 2ouy - hPDE 10a2 catalytic domain (mutant) + AMP
2ouq - hPDE 10a2 catalytic domain + GMP
2ouu - hPDE 10a2 catalytic domain (mutant) + GMP


Cyclic nucleotide PDE

1fsi, 1jh6 – AtPDE – Arabidopsis thaliana
1jh7 – AtPDE + inhibitor
1woj – hPDE residues 166-379
3jyf – PDE residues 16-354 – Klebsiella pneumonia
3v93 – TcPDE catalytic domain – Trypanosoma cruzi
2ilx - rPDE catalytic domain
2xmi, 2y1p, 2y3x - mPDE catalytic domain
2ydb - mPDE catalytic domain + cyclic NADP
3zbr, 3zbs, 3zbz - mPDE catalytic domain (mutant) + NADP
2ydc - mPDE catalytic domain + GTP
2ydd - mPDE catalytic domain + cyclic AMP
2ypc, 2ype, 2yph - mPDE catalytic domain (mutant) + cyclic AMP
2yoz, 2yp0 - mPDE catalytic domain + 2’-AMP
2yq9 - mPDE catalytic domain (mutant) + 2’-AMP
1mc0 – mPDE regulatory subunit
3v94 - TcPDE catalytic domain + inhibitor

Tyrosyl-DNA PDE

1q32 – yPDE – yeast
3sq3, 3sq5, 3sq7, 3sq8 – yPDE (mutant)
1jy1, 1qzq – hPDE residues 149-608
4f1i, 4fva, 4gew – PDE – Caenorhabditis elegans
1mu7 - hPDE residues 149-608 (mutant) + WO4
1mu9 - hPDE residues 149-608 (mutant) + VO4
1nop, 1rff, 1rfi, 1rg1, 1rg2, 1rgt - hPDE residues 149-608 (mutant) + DNA + topoisomerase peptide + VO4
1rgu, 1rh0 - hPDE residues 149-608 (mutant) + polynucleotide + neurohormone
4f1h, 4fpv – PDE + DNA – zebra fish
4gz0, 4gz1, 4gz2 – mPDE + DNA

Glycerophosphodiester PDE

1o1z – PDE – Thermotoga maritima
1t8q, 1ydy – EcPDE
1v8e – TtPDE – Thermus thermophilus
1vd6 – TtPDE + glycerol
1zcc – PDE – Agrobacterium tumefaciens
2o55 – PDE – Galdieria sulphuraria
2oog, 2p76 – PDE – Staphylococcus aureus
2otd – PDE – Shigella flexneri
3ch0 – PDE – Cytophaga hutchisonii
2pz0 – PDE – Thermoanaerobacter tengcongensis
2zo9, 2zoa – PDE + malonate – Enterobacter aerogenes
3mz2, 3no3 – PDE – Parabacterioides distasonia

C-di-GMP PDE

See C-di-GMP phosphodiesterase

2ahd – PDE – Methanocaldococcus jannaschii
3qvq – PDE + glycerol-3-phosphate – Oleispira antarctica
4b2o – PDE – Bacillus subtilis
4g75, 4g76 – PDE – Pseudomonas aeruginosa

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Joel L. Sussman, Rick H. Cote

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