Structural Classification of Proteins
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Fold: Nudix

beta(2)-alpha-beta(3)-alpha; 3 layers: alpha/beta/alpha; mixed sheet
contains beta-grasp motif

Lineage:

  1. Root: scop
  2. Class: Alpha and beta proteins (a+b) [53931]
    Mainly antiparallel beta sheets (segregated alpha and beta regions)
  3. Fold: Nudix [55810]
    beta(2)-alpha-beta(3)-alpha; 3 layers: alpha/beta/alpha; mixed sheet
    contains beta-grasp motif

Superfamilies:

  1. Nudix [55811] (7)
    link to SUPERFAMILY database - Superfamily
    1. MutT-like [55812] (20)
      1. Nucleoside triphosphate pyrophosphorylase (MutT) [55813]
        1. Escherichia coli [TaxId: 562] [55814] (6)
          1. 1pun picpic
            complexed with 8og, mo2
            1. chain a [95133] picpiclink
          2. 1pus picpic
            complexed with 8og, mo2
            1. chain a [95139] picpiclink
          3. 1ppx picpic
            complexed with 8og, mo2
            1. chain a [94981] picpiclink
          4. 1puq picpic
            complexed with 8og, mo2
            1. chain a [95138] picpiclink
          5. 1mut picpic
            1. chain a [40921] picpiclink
          6. 1tum picpic
            complexed with apc, con, mo2; mutant
            1. chain a [40922] picpiclink
      2. Coenzyme A pyrophosphatase [90022]
        1. Deinococcus radiodurans [TaxId: 1299] [90023] (2)
          1. 1nqz picpic
            complexed with mg
            1. chain a [86077] picpiclink
          2. 1nqy picpic
            1. chain a [86076] picpiclink
      3. ADP-ribose pyrophosphatase [64365]
        1. Escherichia coli [TaxId: 562] [64366] (5)
          1. 1g0s picpic
            CASP4
            1. chain a [60187] picpiclink
            2. chain b [60188] picpiclink
          2. 1khz picpic
            complexed with adv, cl, mg
            1. chain a [77414] picpiclink
            2. chain b [77415] picpiclink
          3. 1g9q picpic
            complexed with apr
            1. chain a [60401] picpiclink
            2. chain b [60402] picpiclink
          4. 1ga7 picpic
            complexed with gd3
            1. chain a [60412] picpiclink
            2. chain b [60413] picpiclink
          5. 1viq picpic
            structural genomics
            1. chain a [100766] picpiclink
            2. chain b [100767] picpiclink
            3. chain c [100768] picpiclink
        2. Mycobacterium tuberculosis [TaxId: 1773] [103200] (5)
          gene Rv1700
          1. 1mqe picpic
            complexed with apr, gd3
            1. chain a [91394] picpiclink
          2. 1mk1 picpic
            complexed with apr
            1. chain a [91306] picpiclink
          3. 1mqw picpic
            complexed with adv, mn
            1. chain a [91427] picpiclink
          4. 1mp2 picpic
            1. chain a [91383] picpiclink
          5. 1mr2 picpic
            complexed with a12, mn
            1. chain a [91428] picpiclink
        3. Thermus thermophilus [TaxId: 274] [118083] (11)
          SQ Q84CU3
          1. 1v8y picpic
            complexed with apr, zn; mutant
            1. chain a [113581] picpiclink
          2. 1v8w picpic
            complexed with so4, zn; mutant
            1. chain a [113580] picpiclink
          3. 1v8i picpic
            1. chain a [113572] picpiclink
          4. 1v8r picpic
            complexed with apr, zn
            1. region a:11-169 [119872] picpiclink
          5. 1v8n picpic
            complexed with zn
            1. chain a [113575] picpiclink
          6. 1v8u picpic
            complexed with mg, so4; mutant
            1. chain a [113578] picpiclink
          7. 1v8m picpic
            complexed with apr, gd
            1. chain a [113574] picpiclink
          8. 1v8v picpic
            complexed with apr, mg; mutant
            1. chain a [113579] picpiclink
          9. 1v8l picpic
            complexed with apr
            1. chain a [113573] picpiclink
          10. 1v8s picpic
            complexed with amp, mg
            1. chain a [113576] picpiclink
          11. 1v8t picpic
            complexed with r5p, zn
            1. chain a [113577] picpiclink
      4. ADP-ribose pyrophosphatase homologue YffH [103201]
        1. Escherichia coli [TaxId: 562] [103202] (1)
          1. 1viu picpic
            structural genomics
            1. chain a [100771] picpiclink
            2. chain b [100772] picpiclink
            3. chain c [100773] picpiclink
            4. chain d [100774] picpiclink
      5. ADP compounds hydrolase NudE [103203]
        1. Escherichia coli [TaxId: 562] [103204] (2)
          1. 1vhz picpic
            structural genomics
            complexed with apr
            1. chain a [100718] picpiclink
            2. chain b [100719] picpiclink
          2. 1vhg picpic
            structural genomics
            1. chain a [100672] picpiclink
            2. chain b [100673] picpiclink
      6. NUDT9 (mitochondrial ADP-ribose pyrophosphatase) [103205]
        1. Human (Homo sapiens) [TaxId: 9606] [103206] (2)
          1. 1q33 picpic
            complexed with glc, so4
            1. chain a [95657] picpiclink
          2. 1qvj picpic
            complexed with mg, rp5, so4, trs
            1. chain a [96431] picpiclink
      7. 7,8-dihydro-8-oxoguanine triphosphatase Hmth1 [103207]
        1. Human (Homo sapiens) [TaxId: 9606] [103208] (1)
          1. 1iry picpic
            1. chain a [90690] picpiclink
      8. Hypothetical protein DR1025 [103209]
        1. Deinococcus radiodurans [TaxId: 1299] [103210] (4)
          1. 1sjy picpic
            1. chain a [98900] picpiclink
          2. 1sz3 picpic
            complexed with gnp, mg
            1. chain a [99042] picpiclink
            2. chain b [99043] picpiclink
          3. 1su2 picpic
            complexed with atp, mg
            1. chain a [98991] picpiclink
            2. chain b [98992] picpiclink
          4. 1soi picpic
            complexed with sm
            1. chain a [98941] picpiclink
      9. Diadenosine tetraphosphate hydrolase (Ap4A hydrolase) [64367]
        1. Narrow-leaved blue lupine (Lupinus angustifolius) [TaxId: 3871] [64368] (2)
          1. 1jkn picpic
            complexed with atp
            1. chain a [66808] picpiclink
          2. 1f3y picpic
            mutant
            1. chain a [59635] picpiclink
        2. Caenorhabditis elegans [TaxId: 6239] [75526] (2)
          1. 1ktg picpic
            complexed with amp, mg, oh, po4
            1. chain a [72972] picpiclink
            2. chain b [72973] picpiclink
          2. 1kt9 picpic
            1. chain a [72959] picpiclink
        3. Human (Homo sapiens) [TaxId: 9606] [118084] (3)
          SQ P50583
          1. 1xsb picpic
            mutant
            1. chain a [115923] picpiclink
          2. 1xsa picpic
            mutant
            1. chain a [115922] picpiclink
          3. 1xsc picpic
            complexed with atp; mutant
            1. chain a [115924] picpiclink
      10. Hypothetical protein PAE3301 [75527]
        1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [75528] (3)
          1. 1k2e picpic
            complexed with acy, cry, ni, so4; mutant
            1. chain a [72010] picpiclink
            2. chain b [72011] picpiclink
          2. 1k26 picpic
            complexed with acy, cry, ir3, ni, so4; mutant
            1. chain a [72003] picpiclink
            2. chain b [72004] picpiclink
          3. 1jrk picpic
            structural genomics
            complexed with mpd; mutant
            1. chain a [71827] picpiclink
            2. chain b [71828] picpiclink
            3. chain c [71829] picpiclink
            4. chain d [71830] picpiclink
      11. Hypothetical protein EF1141 [143756]
        1. Enterococcus faecalis [TaxId: 1351] [143757] (1)
          SQ Q836H1 2-148
          1. 2azw picpic
            complexed with 1pe
            1. region a:2-148 [127615] picpiclink
      12. AP6A hydrolase Ndx1 [143758]
        1. Thermus thermophilus [TaxId: 274] [143759] (6)
          SQ Q75UV1 1-126
          1. 1vcd picpic
            automatically matched to 1VC8 A:1-126
            complexed with gol, so4
            1. region a:1-126 [119970] picpiclink
          2. 1vcd picpic
            automatically matched to 1VC8 A:1-126
            complexed with gol, so4
            1. region b:1-126 [119971] picpiclink
          3. 1vc8 picpic
            complexed with 5fa
            1. region a:1-126 [119966] picpiclink
          4. 1vc8 picpic
            automatically matched to 1VC8 A:1-126
            complexed with 5fa
            1. region b:1-126 [119967] picpiclink
          5. 1vc9 picpic
            complexed with atp, mg; mutant
            1. region a:1-126 [119968] picpiclink
          6. 1vc9 picpic
            automatically matched to 1VC9 A:1-126
            complexed with atp, mg; mutant
            1. region b:1-126 [119969] picpiclink
      13. Hypothetical protein NE0184 [143760]
        1. Nitrosomonas europaea [TaxId: 915] [143761] (1)
          SQ Q82XR9 4-149
          1. 2b0v picpic
            complexed with cl, edo, na
            1. region a:4-149 [127650] picpiclink
      14. Hypothetical protein SP1235 (spr1115) [143762]
        1. Streptococcus pneumoniae [TaxId: 1313] [143763] (1)
          SQ Q97QH6 1-155
          1. 2b06 picpic
            complexed with mg
            1. region a:1-155 [127624] picpiclink
      15. U8 snorna-binding protein x29 [143764]
        nuclear decapping enzyme
        1. African clawed frog (Xenopus laevis) [TaxId: 8355] [143765] (12)
          SQ Q6TEC1 14-209
          1. 1u20 picpic
            complexed with gol
            1. region a:14-209 [119463] picpiclink
          2. 1u20 picpic
            automatically matched to 1U20 A:14-209
            complexed with gol
            1. region b:18-209 [119464] picpiclink
          3. 2a8t picpic
            automatically matched to 1U20 A:14-209
            complexed with adn, mgt, mn
            1. region a:18-209 [126418] picpiclink
          4. 2a8t picpic
            automatically matched to 1U20 A:14-209
            complexed with adn, mgt, mn
            1. region b:18-208 [126419] picpiclink
          5. 2a8s picpic
            automatically matched to 1U20 A:14-209
            complexed with gtp, mn, ycm
            1. region a:18-209 [126416] picpiclink
          6. 2a8s picpic
            automatically matched to 1U20 A:14-209
            complexed with gtp, mn, ycm
            1. region b:18-208 [126417] picpiclink
          7. 2a8q picpic
            automatically matched to 1U20 A:14-209
            complexed with mn, pop, ycm
            1. region a:18-209 [126412] picpiclink
          8. 2a8q picpic
            automatically matched to 1U20 A:14-209
            complexed with mn, pop, ycm
            1. region b:18-208 [126413] picpiclink
          9. 2a8r picpic
            automatically matched to 1U20 A:14-209
            complexed with mn, pop, ycm
            1. region a:20-209 [126414] picpiclink
          10. 2a8r picpic
            automatically matched to 1U20 A:14-209
            complexed with mn, pop, ycm
            1. region b:18-208 [126415] picpiclink
          11. 2a8p picpic
            automatically matched to 1U20 A:14-209
            complexed with mn, ycm
            1. region a:18-209 [126410] picpiclink
          12. 2a8p picpic
            automatically matched to 1U20 A:14-209
            complexed with mn, ycm
            1. region b:17-209 [126411] picpiclink
      16. Diphosphoinositol polyphosphate phosphohydrolase [143766]
        1. Human (Homo sapiens) [TaxId: 9606] [143767] (2)
          SQ O95989 8-142
          1. 2fvv picpic
            complexed with cl, ihp, so4
            1. region a:8-142 [134226] picpiclink
          2. 2q9p picpic
            automatically matched to d2fvva1
            complexed with cl, f, ihp, mg
            1. region a:10-141 [150155] picpiclink
    2. MutY C-terminal domain-like [103211] (2)
      1. Adenine glycosylase MutY, C-terminal domain [103212]
        1. Bacillus stearothermophilus [TaxId: 1422] [103213] (3)
          1. 1rrq picpicxref
            complexed with 8og, ca, fs4; mutant
            1. region a:234-360 [97799] picpiclink
          2. 1rrs picpicxref
            complexed with 8og, ca, fs4, hpd; mutant
            1. region a:234-360 [97801] picpiclink
          3. 1vrl picpicxref
            automatically matched to d1rrta2
            complexed with 8og, ade, ca, hpd, sf4; mutant
            1. region a:231-360 [120471] picpiclink
      2. A/G-specific adenine DNA glycosylase [143768]
        MutY homolog
        1. Human (Homo sapiens) [TaxId: 9606] [143769] (1)
          SQ Q9UIF7 356-497
          1. 1x51 picpic
            1. region a:8-149 [121702] picpiclink
    3. NADH pyrophosphatase [103214] (1)
      duplication: consists of two structurally similar domains separated by a rubredoxin-like zinc finger; the N-terminal domain has a rudiment Nudix fold, the C-terminal, probably catalytic, domain has the canonical fold
      1. NADH pyrophosphatase [103215]
        1. Escherichia coli [TaxId: 562] [103216] (1)
          1. 1vk6 picpicxref
            structural genomics
            complexed with mpd, zn
            1. region a:0-96 [111609] picpiclink
            2. region a:126-256 [100852] picpiclink
    4. IPP isomerase-like [64369] (4)
      1. Isopentenyl diphosphate isomerase [64370]
        1. Escherichia coli [TaxId: 562] [64371] (25)
          SQ Q46822
          1. 1hzt picpic
            1. chain a [61459] picpiclink
          2. 1ppv picpic
            complexed with bhi, mg, mn
            1. chain a [104282] picpiclink
            2. chain b [104283] picpiclink
          3. 1r67 picpic
            complexed with mg; mutant
            1. chain a [97147] picpiclink
          4. 1pvf picpic
            complexed with dpo, mg, mn
            1. chain a [104323] picpiclink
            2. chain b [104324] picpiclink
          5. 1x84 picpic
            automatically matched to d1nfsb_
            complexed with mg, mn, sbh
            1. region a:4-179 [121795] picpiclink
          6. 1x84 picpic
            automatically matched to d1nfsb_
            complexed with mg, mn, sbh
            1. region b:4-179 [121796] picpiclink
          7. 1nfz picpic
            complexed with eip, mg, mn
            1. chain a [85658] picpiclink
            2. chain b [85659] picpiclink
          8. 1x83 picpic
            complexed with mg, mn, sbh; mutant
            1. region a:4-179 [121793] picpiclink
          9. 1x83 picpic
            automatically matched to 1X83 A:4-179
            complexed with mg, mn, sbh; mutant
            1. region b:4-179 [121794] picpiclink
          10. 1q54 picpic
            complexed with bhi, mg, mn; mutant
            1. chain a [95860] picpiclink
            2. chain b [95861] picpiclink
          11. 2g74 picpic
            automatically matched to 1X83 A:4-179
            complexed with mg, mn; mutant
            1. region a:4-179 [134728] picpiclink
          12. 2g74 picpic
            automatically matched to 1X83 A:4-179
            complexed with mg, mn; mutant
            1. region b:4-179 [134729] picpiclink
          13. 1nfs picpic
            complexed with ded, mg, mn
            1. chain a [85640] picpiclink
            2. chain b [85641] picpiclink
          14. 2b2k picpic
            automatically matched to 1X83 A:4-179
            complexed with eip, mg, mn; mutant
            1. region a:4-179 [127708] picpiclink
          15. 2b2k picpic
            automatically matched to 1X83 A:4-179
            complexed with eip, mg, mn; mutant
            1. region b:4-179 [127709] picpiclink
          16. 1hx3 picpic
            complexed with imd, mn, so4; mutant
            1. chain a [61351] picpiclink
            2. chain b [61352] picpiclink
          17. 2g73 picpic
            automatically matched to 1X83 A:4-179
            complexed with eip, mg, mn; mutant
            1. region a:4-179 [134726] picpiclink
          18. 2g73 picpic
            automatically matched to 1X83 A:4-179
            complexed with eip, mg, mn; mutant
            1. region b:4-179 [134727] picpiclink
          19. 2vnq picpic
            automatically matched to d1nfsb_
            complexed with imd, mn, so4
            1. region a:4-179 [153341] picpiclink
          20. 2vnq picpic
            automatically matched to d1nfsb_
            complexed with imd, mn, so4
            1. region b:4-179 [153342] picpiclink
          21. 1ow2 picpic
            complexed with eip, mg, mn; mutant
            1. chain a [93626] picpiclink
            2. chain b [93627] picpiclink
          22. 2vnp picpic
            automatically matched to d1nfsb_
            complexed with ded, mg, mn
            1. region a:4-179 [153339] picpiclink
          23. 2vnp picpic
            automatically matched to d1nfsb_
            complexed with ded, mg, mn
            1. region b:4-179 [153340] picpiclink
          24. 1ppw picpic
            complexed with eip, mg, mn
            1. chain a [104284] picpiclink
            2. chain b [104285] picpiclink
          25. 1i9a picpic
            complexed with mn
            1. chain a [62082] picpiclink
            2. chain b [62083] picpiclink
      2. Hypothetical protein DR0079 [103217]
        1. Deinococcus radiodurans [TaxId: 1299] [103218] (1)
          1. 1q27 picpic
            structural genomics
            1. chain a [95621] picpiclink
        2. Deinococcus radiodurans str. R1 (Deinococcus radiodurans R1) [TaxId: 243230] [160692] (2)
          1. 2o5f picpic
            automatically matched to d1q27a_
            1. region a:7-168 [148596] picpiclink
          2. 2o5f picpic
            automatically matched to d1q27a_
            1. region b:7-168 [148597] picpiclink
      3. Hypothetical protein YfcD [143770]
        1. Escherichia coli [TaxId: 562] [143771] (3)
          SQ P65556 8-168
          1. 2fkb picpic
            complexed with act, gol, mg, so4
            1. region a:8-168 [133650] picpiclink
          2. 2fkb picpic
            automatically matched to 2FKB A:8-168
            complexed with act, gol, mg, so4
            1. region b:8-168 [133651] picpiclink
          3. 2fkb picpic
            automatically matched to 2FKB A:8-168
            complexed with act, gol, mg, so4
            1. region c:8-168 [133652] picpiclink
    5. GDP-mannose mannosyl hydrolase NudD [111132] (1)
      1. GDP-mannose mannosyl hydrolase NudD [111133]
        1. Escherichia coli [TaxId: 562] [111134] (5)
          SQ P32056
          1. 1rya picpic
            complexed with cl, gdp, mg, trs
            1. chain a [105122] picpiclink
            2. chain b [105123] picpiclink
          2. 2gt2 picpic
            automatically matched to d1ryaa_
            1. region a:3-160 [135619] picpiclink
          3. 2gt2 picpic
            automatically matched to d1ryaa_
            1. region b:5-160 [135620] picpiclink
          4. 2gt2 picpic
            automatically matched to d1ryaa_
            1. region c:3-160 [135621] picpiclink
          5. 2gt2 picpic
            automatically matched to d1ryaa_
            1. region d:4-160 [135622] picpiclink
    6. BT0354 N-terminal domain-like [143772] (2)
      accosiated with the C-terminal "winged helix" domain (scop_sf 46785)
      1. Hypothetical protein EF2700, N-terminal domain [143773]
        includes extra N-terminal alpha-hairpin, separated by a linker peptide
        1. Enterococcus faecalis [TaxId: 1351] [143774] (2)
          SQ Q830S2 3-204
          1. 2fml picpicxrefxref
            complexed with gol
            1. region a:3-204 [133779] picpiclink
          2. 2fml picpicxrefxref
            automatically matched to 2FML A:3-204
            complexed with gol
            1. region b:4-204 [133781] picpiclink
      2. Hypothetical protein BT0354, N-terminal domain [143775]
        1. Bacteroides thetaiotaomicron [TaxId: 818] [143776] (4)
          SQ Q8AAV8 3-149
          1. 2fb1 picpicxrefxrefxrefxref
            complexed with po4
            1. region a:3-149 [133226] picpiclink
          2. 2fb1 picpicxrefxrefxrefxref
            automatically matched to 2FB1 A:3-149
            complexed with po4
            1. region b:3-149 [133228] picpiclink
          3. 2fb1 picpicxrefxrefxrefxref
            automatically matched to 2FB1 A:3-149
            complexed with po4
            1. region c:3-149 [133230] picpiclink
          4. 2fb1 picpicxrefxrefxrefxref
            automatically matched to 2FB1 A:3-149
            complexed with po4
            1. region d:3-149 [133232] picpiclink
    7. mRNA decapping enzyme-like [143777] (1)
      part of Pfam 00293
      1. mRNA decapping enzyme Dcp2p catalytic domain [143778]
        1. Schizosaccharomyces pombe [TaxId: 4896] [143779] (1)
          SQ O13828 95-245
          1. 2a6t picpicxref
            1. region a:95-245 [126310] picpiclink
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MRC site 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