Phosphodiesterase

From Proteopedia

Revision as of 12:13, 11 November 2012

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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.

3D Structures of phosphodiesterase

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
2ju4 - PDE γ subunit – bovine - NMR

PDE 1

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

PDE 2

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

PDE 3

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

PDE 4a

3i8v – 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 - 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, 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 - 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 – hPDE 5a1 catalytic domain (mutant) + 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

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 – hPDE 9a catalytic domain + inhibitor
3n3z, 3qi3, 3qi4 - hPDE 9a catalytic domain (mutant) + inhibitor
3dy8, 3dyl, 3dyn, 3dyq, 3dys - hPDE 9 catalytic domain + GMP

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 - hPDE 10a catalytic domain + inhibitor
2wey, 3hqw, 3hqy, 3hqz, 3hr1, 3ui7 - hPDE 10a catalytic domain + 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
2ilx - rPDE catalytic domain
2xmi, 2y1p - mPDE catalytic domain + citrate

Tyrosyl-DNA PDE

1q32 – yPDE – yeast
3sq3, 3sq5, 3sq7, 3sq8 – yPDE (mutant)
1jy1, 1qzq – hPDE residues 149-608
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

Glycerophosphodiester PDE

1o1z – PDE – Thermotoga maritima
1t8q, 1ydy – PDE – Escherichia coli
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
1ahd – PDE – Methanocaldococcus jannaschii
3qvq – PDE + glycerol-3-phosphate – Oleispira antarctica