Fold: HD-domain/PDEase-like

multihelical; consists of two different alpha-helical bundles

Lineage:

1. Root: scop
2. Class: All alpha proteins [46456]
3. Fold: HD-domain/PDEase-like [109603]
   multihelical; consists of two different alpha-helical bundles

Superfamilies:

1. HD-domain/PDEase-like [109604] (5)
   uperfamily
   1. HD domain [101340] (13)
      Pfam 01966; metal dependent phosphohydrolases
      1. Stringent response-like protein RelA N-terminal domain [101341]
         1. Streptococcus equisimilis [TaxId: 119602] [101342] (1)
            1. 1vj7
               complexed with gdp, gpx, mn
               1. region a:5-196 [100801]
               2. region b:5-196 [100803]
      2. 5'-nucleotidase YfbR [116969]
         1. Escherichia coli [TaxId: 562] [116970] (2)
            SQ P76491
            Structural genomics target
            1. 2paq
               automatically matched to d1wpha_
               1. region a:2-187 [139643]
            2. 2paq
               automatically matched to d1wpha_
               1. region b:2-187 [139644]
      3. Oxetanocin-like protein PF0395 [116971]
         similar fold and oligomeric structure to 5'-nucleotidase YfbR
         1. Pyrococcus furiosus [TaxId: 2261] [116972] (1)
            SQ Q8U3R1
            1. 1xx7
               Structural genomics target
               complexed with ni, unx
               1. chain a [116143]
               2. chain b [116144]
               3. chain c [116145]
               4. chain d [116146]
               5. chain e [116147]
               6. chain f [116148]
      4. Hypothetical protein AF1432 [140763]
         1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [140764] (4)
            SQ O28840 7-172! SQ O28840 7-173
            1. 1ynb
               1. region a:7-173 [123718]
            2. 1ynb
               automatically matched to 1YNB A:7-173
               1. region b:7-173 [123719]
            3. 1ynb
               automatically matched to 1YNB A:7-173
               1. region c:7-173 [123720]
            4. 1yoy
               1. region a:7-172 [123795]
      5. Hypothetical protein aq_1910 [140765]
         elaborated with additional structures in C-terminal extension
         1. Aquifex aeolicus [TaxId: 63363] [140766] (2)
            SQ O67745 1-369
            1. 2hek
               complexed with br, cl, gdp, gol, po4, zn
               1. region a:1-369 [136354]
            2. 2hek
               automatically matched to 2HEK A:1-369
               complexed with br, cl, gdp, gol, po4, zn
               1. region b:1-369 [136355]
      6. Hypothetical protein EF1143 [140767]
         Probable ortholog of aq_1910
         1. Enterococcus faecalis [TaxId: 1351] [140768] (2)
            SQ Q836G9 1-453
            1. 2o6i
               complexed with cl, hed, zn
               1. region a:1-453 [138920]
            2. 2o6i
               automatically matched to 2O6I A:1-453
               complexed with cl, hed, zn
               1. region b:1-453 [138921]
      7. Predicted hydrolase mes0020 [158719]
         1. Uncultured thermotogales bacterium [TaxId: 221214] [158720] (1)
            SQ Q1EM40 1-217
            1. 2pq7
               complexed with cl, fe, mpd, po4
               1. region a:1-217 [149786]
      8. Uncharacterized protein Lin1889 [158721]
         1. Listeria innocua [TaxId: 1642] [158722] (1)
            SQ Q92AN1 1-201
            1. 3b57
               complexed with mg
               1. region a:1-201 [154835]
      9. Uncharacterized protein SE1688 [158723]
         1. Staphylococcus epidermidis [TaxId: 1282] [158724] (2)
            SQ Q8CRP0 1-216
            1. 2qgs
               complexed with zn
               1. region a:1-216 [150782]
            2. 2qgs
               automatically matched to 2QGS A:1-216
               complexed with zn
               1. region b:1-216 [150783]
      10. Hypothetical protein Atu1052 [158725]
          1. Agrobacterium tumefaciens [TaxId: 358] [158726] (4)
             SQ Q8UGI5 6-205
             1. 2gz4
                1. region a:6-205 [147196]
             2. 2gz4
                automatically matched to 2GZ4 A:6-205
                1. region b:6-203 [147197]
             3. 2gz4
                automatically matched to 2GZ4 A:6-205
                1. region c:6-201 [147198]
             4. 2gz4
                automatically matched to 2GZ4 A:6-205
                1. region d:8-204 [147199]
      11. Uncharacterized protein BH2835 [158727]
          1. Bacillus halodurans [TaxId: 86665] [158728] (4)
             SQ Q9K916 2-213
             1. 3dto
                1. region a:2-213 [157850]
             2. 3dto
                automatically matched to 3DTO A:2-213
                1. region b:2-213 [157851]
             3. 3dto
                automatically matched to 3DTO A:2-213
                1. region c:2-213 [157852]
             4. 3dto
                automatically matched to 3DTO A:2-213
                1. region d:2-213 [157853]
      12. Uncharacterized protein LP2664 [158729]
          1. Lactobacillus plantarum [TaxId: 1590] [158730] (4)
             SQ Q88U62 1-215
             1. 2pjq
                1. region a:1-215 [149569]
             2. 2pjq
                automatically matched to 2PJQ A:1-215
                1. region b:1-215 [149570]
             3. 2pjq
                automatically matched to 2PJQ A:1-215
                1. region c:1-215 [149571]
             4. 2pjq
                automatically matched to 2PJQ A:1-215
                1. region d:1-215 [149572]
      13. Uncharacterized protein BT9727_1981 [158731]
          1. Bacillus thuringiensis [TaxId: 1428] [158732] (2)
             SQ Q6HJG6 2-214
             1. 3djb
                complexed with mg; mutant
                1. region a:2-214 [157756]
             2. 3djb
                automatically matched to 3DJB A:2-214
                complexed with mg; mutant
                1. region b:2-214 [157757]
   2. PDEase [48548] (6)
      Pfam 00233; multihelical; can be divided into three subdomains
      1. Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b [48549]
         1. Human (Homo sapiens) [TaxId: 9606] [48550] (14)
            SQ Q07343 324-667
            1. 1f0j
               complexed with ars, mg, zn; mutant
               1. chain a [19346]
               2. chain b [19347]
            2. 1xm6
               complexed with 5rm, mg, zn
               1. chain a [115471]
               2. chain b [115472]
            3. 1ror
               complexed with amp, zn; mutant
               1. chain a [111901]
               2. chain b [111902]
            4. 1ro6
               complexed with ars, mn, rol, zn; mutant
               1. chain a [111897]
               2. chain b [111898]
            5. 1xlz
               complexed with fil, mg, zn
               1. chain a [115459]
               2. chain b [115460]
            6. 1ro9
               complexed with 8br, zn; mutant
               1. chain a [111899]
               2. chain b [111900]
            7. 1xn0
               complexed with 4rr, 4sr, mg, zn
               1. chain a [115571]
               2. chain b [115572]
            8. 1xmu
               complexed with mg, rof, zn
               1. chain a [115562]
               2. chain b [115563]
            9. 1tb5
               complexed with amp, mg, zn
               1. chain a [106735]
               2. chain b [106736]
            10. 1xos
                complexed with mg, so4, via, zn
                1. chain a [115712]
            11. 1xm4
                complexed with mg, pil, zn
                1. chain a [115465]
                2. chain b [115466]
            12. 1xlx
                complexed with cio, mg, zn
                1. chain a [115455]
                2. chain b [115456]
            13. 1xot
                complexed with mg, vdn, zn
                1. chain a [115713]
                2. chain b [115714]
            14. 1xmy
                complexed with 4rr, mg, zn
                1. chain a [115569]
                2. chain b [115570]
      2. Catalytic domain of cyclic nucleotide phosphodiesterase pde4d [89151]
         1. Human (Homo sapiens) [TaxId: 9606] [89152] (39)
            SQ Q08499 388-713
            1. 1y2k
               automatically matched to d1oyna_
               complexed with 7de, edo, mg, zn
               1. region a:86-411 [122571]
            2. 1y2k
               automatically matched to d1oyna_
               complexed with 7de, edo, mg, zn
               1. region b:86-411 [122572]
            3. 1y2b
               automatically matched to d1oyna_
               complexed with dee, edo, mg, zn
               1. region a:86-411 [122556]
            4. 1y2b
               automatically matched to d1oyna_
               complexed with dee, edo, mg, zn
               1. region b:86-411 [122557]
            5. 1xor
               complexed with mg, zar, zn
               1. chain a [115710]
               2. chain b [115711]
            6. 1xom
               complexed with cio, edo, mg, zn
               1. chain a [115704]
               2. chain b [115705]
            7. 1tb7
               complexed with amp, b3p, edo, mg, zn
               1. chain a [106739]
               2. chain b [106740]
            8. 1tbb
               complexed with edo, mg, rol, zn
               1. chain a [106741]
               2. chain b [106742]
            9. 1y2d
               automatically matched to d1oyna_
               complexed with 4de, b3p, edo, mg, zn
               1. region a:86-411 [122560]
            10. 1y2d
                automatically matched to d1oyna_
                complexed with 4de, b3p, edo, mg, zn
                1. region b:86-411 [122561]
            11. 1y2c
                automatically matched to d1oyna_
                complexed with 3de, edo, mg, zn
                1. region a:86-411 [122558]
            12. 1y2c
                automatically matched to d1oyna_
                complexed with 3de, edo, mg, zn
                1. region b:86-411 [122559]
            13. 1xon
                complexed with b3p, edo, mg, pil, zn
                1. chain a [115706]
                2. chain b [115707]
            14. 2qyn
                automatically matched to d1oyna_
                complexed with mg, npv, zn
                1. region a:86-411 [151475]
            15. 2qyn
                automatically matched to d1oyna_
                complexed with mg, npv, zn
                1. region b:88-411 [151476]
            16. 1xoq
                complexed with edo, mg, rof, zn
                1. chain a [115708]
                2. chain b [115709]
            17. 2qyl
                automatically matched to d1oyna_
                complexed with mg, npv, zn
                1. region a:153-485 [151474]
            18. 1y2e
                automatically matched to d1oyna_
                complexed with 5de, edo, mg, zn
                1. region a:86-411 [122562]
            19. 1y2e
                automatically matched to d1oyna_
                complexed with 5de, edo, mg, zn
                1. region b:88-411 [122563]
            20. 2fm0
                automatically matched to d1oyna_
                complexed with m98, mg, zn
                1. region a:79-412 [133752]
            21. 2fm0
                automatically matched to d1oyna_
                complexed with m98, mg, zn
                1. region b:86-412 [133753]
            22. 2fm0
                automatically matched to d1oyna_
                complexed with m98, mg, zn
                1. region c:86-412 [133754]
            23. 2fm0
                automatically matched to d1oyna_
                complexed with m98, mg, zn
                1. region d:79-412 [133755]
            24. 2fm5
                automatically matched to d1oyna_
                complexed with m99, mg, zn
                1. region a:79-412 [133761]
            25. 2fm5
                automatically matched to d1oyna_
                complexed with m99, mg, zn
                1. region b:86-412 [133762]
            26. 2fm5
                automatically matched to d1oyna_
                complexed with m99, mg, zn
                1. region c:86-412 [133763]
            27. 2fm5
                automatically matched to d1oyna_
                complexed with m99, mg, zn
                1. region d:79-412 [133764]
            28. 1oyn
                complexed with rol, zn
                1. chain a [87609]
                2. chain b [87610]
                3. chain c [87611]
                4. chain d [87612]
            29. 1zkn
                automatically matched to d1oyna_
                complexed with ibm, mg, zn
                1. region a:79-412 [125201]
            30. 1zkn
                automatically matched to d1oyna_
                complexed with ibm, mg, zn
                1. region b:86-412 [125202]
            31. 1zkn
                automatically matched to d1oyna_
                complexed with ibm, mg, zn
                1. region c:83-412 [125203]
            32. 1zkn
                automatically matched to d1oyna_
                complexed with ibm, mg, zn
                1. region d:79-412 [125204]
            33. 1q9m
                complexed with rol, zn
                1. chain a [96288]
                2. chain b [96289]
                3. chain c [96290]
                4. chain d [96291]
            34. 1ptw
                complexed with amp, zn
                1. chain a [95106]
                2. chain b [95107]
                3. chain c [95108]
                4. chain d [95109]
            35. 1y2h
                automatically matched to d1mkda_
                complexed with 6de, mg, zn
                1. region a:163-485 [122567]
            36. 1y2h
                automatically matched to d1mkda_
                complexed with 6de, mg, zn
                1. region b:163-485 [122568]
            37. 1mkd
                complexed with mg, zar, zn
                1. chain a [84982]
                2. chain b [84983]
                3. chain c [84984]
                4. chain d [84985]
                5. chain e [84986]
                6. chain f [84987]
                7. chain g [84988]
                8. chain h [84989]
                9. chain i [84990]
                10. chain j [84991]
                11. chain k [84992]
                12. chain l [84993]
            38. 1y2j
                automatically matched to d1mkda_
                complexed with 7de, mg, zn
                1. region a:163-485 [122569]
            39. 1y2j
                automatically matched to d1mkda_
                complexed with 7de, mg, zn
                1. region b:163-485 [122570]
      3. cGMP-specific 3',5'-cyclic phosphodiesterase pde5a1-Ibmx [101439]
         1. Human (Homo sapiens) [TaxId: 9606] [101440] (18)
            SQ O76074 534-860
            1. 1tbf
               complexed with gol, mg, via, zn
               1. chain a [106743]
            2. 1xoz
               complexed with cia, mg, zn
               1. chain a [115719]
            3. 2chm
               complexed with 3p4, mes, mg, zn
               1. region a:537-858 [130472]
            4. 1xp0
               complexed with mg, vdn, zn
               1. chain a [115720]
            5. 2h44
               automatically matched to d1t9ra_
               complexed with 7ca, mg, zn
               1. region a:535-860 [136069]
            6. 2h40
               automatically matched to d1t9ra_
               complexed with mg, zn
               1. region a:535-860 [136063]
            7. 1t9s
               complexed with 5gp, mg, zn
               1. chain a [106726]
               2. chain b [106727]
            8. 3bjc
               automatically matched to d1t9ra_
               complexed with mg, wan, zn
               1. region a:535-860 [155329]
            9. 3b2r
               automatically matched to d1t9ra_
               complexed with vdn
               1. region a:535-860 [154768]
            10. 3b2r
                automatically matched to d1t9ra_
                complexed with vdn
                1. region b:538-860 [154769]
            11. 1rkp
                complexed with ibm, mg, zn; mutant
                1. chain a [97620]
            12. 1t9r
                complexed with cit, po4, zn
                1. chain a [106725]
            13. 2h42
                automatically matched to d1t9ra_
                complexed with mg, via, zn
                1. region a:535-860 [136064]
            14. 2h42
                automatically matched to d1t9ra_
                complexed with mg, via, zn
                1. region b:535-860 [136065]
            15. 2h42
                automatically matched to d1t9ra_
                complexed with mg, via, zn
                1. region c:535-860 [136066]
            16. 1udt
                complexed with mg, via, zn
                1. chain a [99221]
            17. 1uho
                complexed with mg, vdn, zn
                1. chain a [107851]
            18. 1udu
                complexed with cia, mg, zn
                1. chain a [99222]
                2. chain b [99223]
      4. cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b [101441]
         1. Human (Homo sapiens) [TaxId: 9606] [101442] (2)
            1. 1so2
               complexed with 666, hg9, mg
               1. chain a [98936]
               2. chain b [98937]
               3. chain c [98938]
               4. chain d [98939]
            2. 1soj
               complexed with ibm, mg
               1. chain a [98942]
               2. chain b [98943]
               3. chain c [98944]
               4. chain d [98945]
               5. chain e [98946]
               6. chain f [98947]
               7. chain g [98948]
               8. chain h [98949]
               9. chain i [98950]
               10. chain j [98951]
               11. chain k [98952]
               12. chain l [98953]
      5. High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A, PDE9A [109942]
         1. Human (Homo sapiens) [TaxId: 9606] [109943] (14)
            SQ O76083 241-566
            1. 3dy8
               automatically matched to d2hd1a1
               complexed with 5gp, fmt, ibm, mg, mn
               1. region a:182-505 [157937]
            2. 3dy8
               automatically matched to d2hd1a1
               complexed with 5gp, fmt, ibm, mg, mn
               1. region b:182-505 [157938]
            3. 3dyn
               automatically matched to d2hd1a1
               complexed with ibm, mg, pcg, zn
               1. region a:182-505 [157942]
            4. 3dyn
               automatically matched to d2hd1a1
               complexed with ibm, mg, pcg, zn
               1. region b:182-505 [157943]
            5. 3dys
               automatically matched to d2hd1a1
               complexed with 5gp, fmt, ibm, mg, mn
               1. region a:182-505 [157946]
            6. 3dys
               automatically matched to d2hd1a1
               complexed with 5gp, fmt, ibm, mg, mn
               1. region b:182-505 [157947]
            7. 2hd1
               automatically matched to d1tbma_
               complexed with ibm, mg, zn
               1. region a:181-506 [136338]
            8. 2hd1
               automatically matched to d1tbma_
               complexed with ibm, mg, zn
               1. region b:181-506 [136339]
            9. 3dyq
               automatically matched to d2hd1a1
               complexed with ibm, na, pcg
               1. region a:182-505 [157944]
            10. 3dyq
                automatically matched to d2hd1a1
                complexed with ibm, na, pcg
                1. region b:182-505 [157945]
            11. 3dyl
                automatically matched to d2hd1a1
                complexed with fmt, ibm, mg, mn, pcg
                1. region a:182-505 [157940]
            12. 3dyl
                automatically matched to d2hd1a1
                complexed with fmt, ibm, mg, mn, pcg
                1. region b:182-505 [157941]
            13. 2yy2
                automatically matched to d2hd1a1
                complexed with ibm, mg, zn
                1. region a:181-506 [153829]
            14. 2yy2
                automatically matched to d2hd1a1
                complexed with ibm, mg, zn
                1. region b:181-504 [153830]
      6. Catalytic domain of cyclic nucleotide phosphodiesterase 1b, PDE1B [109944]
         1. Human (Homo sapiens) [TaxId: 9606] [109945] (1)
            SQ Q01064 126-482
            1. 1taz
               complexed with mg, zn
               1. chain a [106734]
   3. modified HD domain [116973] (1)
      retains the superfamily core fold but lacks the conserved metal-binding site
      1. Hypothetical protein Cj0248 [116974]
         1. Campylobacter jejuni [TaxId: 197] [116975] (1)
            SQ Q9PIP7
            1. 1vqr
               Structural genomics target
               1. chain a [114015]
               2. chain b [114016]
               3. chain c [114017]
               4. chain d [114018]
   4. MioX-like [140769] (2)
      Pfam 05153; DUF706
      1. Myo-inositol oxygenase MioX [140770]
         1. Human (Homo sapiens) [TaxId: 9606] [140771] (2)
            SQ Q9UGB7 37-285
            1. 2ibn
               complexed with cys, fe, i1n, so4
               1. region a:37-285 [137195]
            2. 2ibn
               automatically matched to 2IBN A:37-285
               complexed with cys, fe, i1n, so4
               1. region b:37-285 [137196]
         2. Mouse (Mus musculus) [TaxId: 10090] [140772] (2)
            SQ Q9QXN5 28-285
            1. 3bxd
               automatically matched to d2huoa1
               complexed with fe, fmt, ins, oh
               1. region a:28-285 [155707]
            2. 2huo
               complexed with fe, fmt, ins, oh
               1. region a:28-285 [136778]
   5. Ppx associated domain [140773] (1)
      this domain is C-terminal to Ppx domain in some Exopolyphosphatases
      1. Exopolyphosphatase Ppx C-terminal domain [140774]
         1. Escherichia coli [TaxId: 562] [140775] (6)
            SQ P0AFL6 312-508
            1. 1u6z
               complexed with so4
               1. region a:313-509 [119608]
            2. 1u6z
               automatically matched to 1U6Z A:313-509
               complexed with so4
               1. region b:313-509 [119611]
            3. 2flo
               automatically matched to 1U6Z A:313-509
               1. region a:313-506 [133733]
            4. 2flo
               automatically matched to 1U6Z A:313-509
               1. region b:313-506 [133736]
            5. 2flo
               automatically matched to 1U6Z A:313-509
               1. region c:313-506 [133739]
            6. 2flo
               automatically matched to 1U6Z A:313-509
               1. region d:313-506 [133742]

Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009 Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk