Structural Classification of Proteins
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Fold: Ribokinase-like

core: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest
potential superfamily: members of this fold have similar functions but different ATP-binding sites

Lineage:

  1. Root: scop
  2. Class: Alpha and beta proteins (a/b) [51349]
    Mainly parallel beta sheets (beta-alpha-beta units)
  3. Fold: Ribokinase-like [53612]
    core: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest
    potential superfamily: members of this fold have similar functions but different ATP-binding sites

Superfamilies:

  1. Ribokinase-like [53613] (5)
    has extra strand located between strands 2 and 3
    link to SUPERFAMILY database - Superfamily
    1. Thiamin biosynthesis kinases [53620] (4)
      1. Hydroxyethylthiazole kinase (THZ kinase, ThiK) [53621]
        1. Bacillus subtilis [TaxId: 1423] [53622] (5)
          1. 1ekq picpic
            mutant
            1. chain a [34941] picpiclink
            2. chain b [34942] picpiclink
          2. 1esj picpic
            complexed with so4; mutant
            1. region a:1-272 [34943] picpiclink
            2. region b:1-272 [34944] picpiclink
            3. region c:1-272 [34945] picpiclink
          3. 1ekk picpic
            complexed with so2, tze; mutant
            1. chain a [34946] picpiclink
            2. chain b [34947] picpiclink
          4. 1c3q picpic
            complexed with cl, tze
            1. region a:1-272 [118436] picpiclink
            2. region b:1-272 [118437] picpiclink
            3. region c:1-272 [118438] picpiclink
          5. 1esq picpic
            complexed with atp, mg, so4, thq; mutant
            1. region a:1-272 [34951] picpiclink
            2. region b:1-271 [34952] picpiclink
            3. region c:1-272 [34953] picpiclink
        2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102637] (1)
          1. 1v8a picpic
            complexed with cl, zn
            1. chain a [100494] picpiclink
      2. 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMP-phosphate kinase, ThiD) [69589]
        1. Salmonella typhimurium [TaxId: 90371] [69590] (2)
          1. 1jxh picpic
            complexed with so4
            1. chain a [67415] picpiclink
            2. chain b [67416] picpiclink
          2. 1jxi picpic
            complexed with hmh, so4
            1. chain a [67417] picpiclink
            2. chain b [67418] picpiclink
        2. Thermus thermophilus [TaxId: 274] [89775] (1)
          1. 1ub0 picpic
            structural genomics
            complexed with dox, gol, so4
            1. chain a [88394] picpiclink
    2. YjeF C-terminal domain-like [75292] (2)
      1. Hypothetical protein YxkO [75293]
        1. Bacillus subtilis [TaxId: 1423] [75294] (1)
          1. 1kyh picpic
            structural genomics
            complexed with mse
            1. chain a [73222] picpiclink
      2. Hypothetical protein TM0922, C-terminal domain [142707]
        YjeF homolog
        1. Thermotoga maritima [TaxId: 2336] [142708] (1)
          SQ Q9X024 212-489
          1. 2ax3 picpicxref
            complexed with gol
            1. region a:212-489 [127477] picpiclink
    3. PfkB-like kinase [82515] (2)
      includes a variety of carbohydrate and pyrimidine kinases
      1. Pyridoxal kinase [82516]
        1. Sheep (Ovis aries) [TaxId: 9940] [82517] (8)
          1. 1lhp picpic
            1. chain a [77960] picpiclink
            2. chain b [77961] picpiclink
          2. 1lhr picpic
            complexed with atp, k, zn
            1. chain a [77962] picpiclink
            2. chain b [77963] picpiclink
          3. 1rfv picpic
            complexed with adp, zn2
            1. chain a [97409] picpiclink
            2. chain b [97410] picpiclink
          4. 1ygj picpic
            automatically matched to d1rfua_
            complexed with rmc
            1. region a:4-312 [123144] picpiclink
          5. 1rft picpic
            complexed with acp, k, pxm, zn2
            1. chain a [97400] picpiclink
          6. 1rfu picpic
            complexed with adp, plp, zn2
            1. chain a [97401] picpiclink
            2. chain b [97402] picpiclink
            3. chain c [97403] picpiclink
            4. chain d [97404] picpiclink
            5. chain e [97405] picpiclink
            6. chain f [97406] picpiclink
            7. chain g [97407] picpiclink
            8. chain h [97408] picpiclink
          7. 1yhj picpic
            automatically matched to d1rfua_
            complexed with r6c
            1. region a:6-312 [123177] picpiclink
          8. 1ygk picpic
            automatically matched to d1rfua_
            complexed with rrc
            1. region a:4-312 [123145] picpiclink
      2. Pyridoxamine kinase [102638]
        1. Escherichia coli [TaxId: 562] [102639] (2)
          SQ P77150
          1. 1vi9 picpic
            structural genomics
            complexed with bme, so4
            1. chain a [100750] picpiclink
            2. chain b [100751] picpiclink
            3. chain c [100752] picpiclink
            4. chain d [100753] picpiclink
          2. 1td2 picpic
            complexed with pxl, so4
            1. chain a [106765] picpiclink
            2. chain b [106766] picpiclink
    4. Ribokinase-like [53614] (13)
      1. Ribokinase [53615]
        1. Escherichia coli [TaxId: 562] [53616] (5)
          1. 1rkd picpic
            complexed with adp, po4, rib
            1. chain a [34928] picpiclink
          2. 1rka picpic
            1. chain a [34929] picpiclink
          3. 1rk2 picpic
            complexed with adp, alf, mg, rib
            1. chain a [34930] picpiclink
            2. chain b [34931] picpiclink
            3. chain c [34932] picpiclink
            4. chain d [34933] picpiclink
          4. 1rks picpic
            complexed with po4, rib
            1. chain a [34934] picpiclink
          5. 1gqt picpic
            complexed with acp, cs, rib
            1. chain a [65472] picpiclink
            2. chain b [65473] picpiclink
            3. chain c [65474] picpiclink
            4. chain d [65475] picpiclink
        2. Thermotoga maritima [TaxId: 2336] [110706] (1)
          SQ Q9X055
          1. 1vm7 picpic
            Structural genomics target
            1. chain a [108884] picpiclink
            2. chain b [108885] picpiclink
        3. Human (Homo sapiens) [TaxId: 9606] [142709] (2)
          SQ Q9H477 15-322
          1. 2fv7 picpic
            complexed with adp, mg, na, unx
            1. region a:15-322 [134197] picpiclink
          2. 2fv7 picpic
            automatically matched to 2FV7 A:15-322
            complexed with adp, mg, na, unx
            1. region b:15-322 [134198] picpiclink
      2. 2-keto-3-deoxygluconate kinase [75295]
        1. Thermotoga maritima, TM0067 [TaxId: 2336] [75296] (2)
          1. 2afb picpic
            automatically matched to d1j5va_
            complexed with ca, ni; mutant
            1. region a:-2-330 [126674] picpiclink
          2. 2afb picpic
            automatically matched to d1j5va_
            complexed with ca, ni; mutant
            1. region b:0-330 [126675] picpiclink
        2. Thermus thermophilus [TaxId: 274] [102640] (4)
          1. 1v1a picpic
            structural genomics
            complexed with adp, kdg
            1. chain a [100249] picpiclink
            2. chain b [100250] picpiclink
          2. 1v19 picpic
            structural genomics
            complexed with dox
            1. chain a [100247] picpiclink
            2. chain b [100248] picpiclink
          3. 1v1b picpic
            structural genomics
            complexed with atp
            1. chain a [100251] picpiclink
            2. chain b [100252] picpiclink
            3. chain c [100253] picpiclink
            4. chain d [100254] picpiclink
          4. 1v1s picpic
            structural genomics
            1. chain a [100256] picpiclink
            2. chain b [100257] picpiclink
            3. chain c [100258] picpiclink
            4. chain d [100259] picpiclink
            5. chain e [100260] picpiclink
            6. chain f [100261] picpiclink
      3. Hypothetical protein TM0415 [102641]
        1. Thermotoga maritima [TaxId: 2336] [102642] (1)
          1. 1vk4 picpic
            structural genomics
            1. chain a [100850] picpiclink
      4. Putative sugar kinase TM0828 [82518]
        1. Thermotoga maritima [TaxId: 2336] [82519] (2)
          1. 2ajr picpic
            automatically matched to d1o14a_
            complexed with act, mg
            1. region a:1-319 [126892] picpiclink
          2. 2ajr picpic
            automatically matched to d1o14a_
            complexed with act, mg
            1. region b:1-319 [126893] picpiclink
      5. Adenosine kinase [53617]
        1. Human (Homo sapiens) [TaxId: 9606] [53618] (5)
          1. 1bx4 picpic
            complexed with adn, cl, mo4, mo6
            1. chain a [34935] picpiclink
          2. 2i6a picpic
            automatically matched to d1bx4a_
            complexed with 5i5
            1. region a:4-345 [137091] picpiclink
          3. 2i6a picpic
            automatically matched to d1bx4a_
            complexed with 5i5
            1. region b:4-345 [137092] picpiclink
          4. 2i6a picpic
            automatically matched to d1bx4a_
            complexed with 5i5
            1. region c:4-345 [137093] picpiclink
          5. 2i6a picpic
            automatically matched to d1bx4a_
            complexed with 5i5
            1. region d:4-345 [137094] picpiclink
        2. Toxoplasma gondii [TaxId: 5811] [53619] (10)
          1. 2abs picpic
            complexed with acp, cl, na; mutant
            1. region a:10-359 [126534] picpiclink
          2. 2a9y picpic
            automatically matched to 2ABS A:10-359
            complexed with 26a, act, cl, na; mutant
            1. region a:10-359 [126460] picpiclink
          3. 2a9z picpic
            automatically matched to 2ABS A:10-359
            complexed with 26a, acp, cl, na; mutant
            1. region a:10-359 [126461] picpiclink
          4. 2ab8 picpic
            automatically matched to 2ABS A:10-359
            complexed with acp, cl, mtp, na; mutant
            1. region a:10-359 [126515] picpiclink
          5. 2aa0 picpic
            automatically matched to 2ABS A:10-359
            complexed with act, cl, mtp, na; mutant
            1. region a:10-359 [126462] picpiclink
          6. 1dgm picpic
            complexed with acy, adn, cl, mg; mutant
            1. chain a [34936] picpiclink
          7. 1lii picpic
            complexed with acp, adn, cl, mg
            1. chain a [73921] picpiclink
          8. 1lij picpic
            complexed with acp, cl, mg, rpp
            1. chain a [73922] picpiclink
          9. 1lik picpic
            complexed with adn, cl, so4
            1. chain a [73923] picpiclink
          10. 1lio picpic
            1. chain a [73924] picpiclink
      6. Aminoimidazole riboside kinase [117720]
        1. Salmonella typhimurium [TaxId: 90371] [117721] (3)
          SQ Q8ZKR2
          1. 1tyy picpic
            complexed with k
            1. chain a [112850] picpiclink
            2. chain b [112851] picpiclink
          2. 1tz6 picpic
            complexed with acp, ais, k, mg
            1. chain a [112862] picpiclink
            2. chain b [112863] picpiclink
          3. 1tz3 picpic
            complexed with ais, k
            1. chain a [112860] picpiclink
            2. chain b [112861] picpiclink
      7. Tagatose-6-phosphate kinase LacC [142710]
        1. Enterococcus faecalis [TaxId: 1351] [142711] (4)
          SQ Q833W9 1-313
          1. 2f02 picpic
            automatically matched to 2AWD A:1-313
            complexed with atp
            1. region a:1-313 [132649] picpiclink
          2. 2f02 picpic
            automatically matched to 2AWD A:1-313
            complexed with atp
            1. region b:1-313 [132650] picpiclink
          3. 2awd picpic
            complexed with br
            1. region a:1-313 [127430] picpiclink
          4. 2awd picpic
            automatically matched to 2AWD A:1-313
            complexed with br
            1. region b:1-312 [127431] picpiclink
      8. Fructose 1-phosphate kinase FruB [142712]
        1. Bacillus halodurans [TaxId: 86665] [142713] (2)
          SQ Q9KEM5 1-306
          1. 2abq picpic
            complexed with po4
            1. region a:1-306 [126528] picpiclink
          2. 2abq picpic
            automatically matched to 2ABQ A:1-306
            complexed with po4
            1. region b:1-306 [126529] picpiclink
      9. Hypothetical fructokinase ST2478 [142714]
        1. Sulfolobus tokodaii [TaxId: 111955] [142715] (18)
          SQ Q96XN9 2-309
          1. 2dcn picpic
            complexed with adp, ckp, k, mg
            1. region a:2-309 [131374] picpiclink
          2. 2dcn picpic
            automatically matched to 2DCN A:2-309
            complexed with adp, ckp, k, mg
            1. region b:2-309 [131375] picpiclink
          3. 2dcn picpic
            automatically matched to 2DCN A:2-309
            complexed with adp, ckp, k, mg
            1. region c:2-309 [131376] picpiclink
          4. 2dcn picpic
            automatically matched to 2DCN A:2-309
            complexed with adp, ckp, k, mg
            1. region d:2-309 [131377] picpiclink
          5. 2dcn picpic
            automatically matched to 2DCN A:2-309
            complexed with adp, ckp, k, mg
            1. region e:2-309 [131378] picpiclink
          6. 2dcn picpic
            automatically matched to 2DCN A:2-309
            complexed with adp, ckp, k, mg
            1. region f:2-309 [131379] picpiclink
          7. 2dcn picpic
            automatically matched to 2DCN A:2-309
            complexed with adp, ckp, k, mg
            1. region g:2-309 [131380] picpiclink
          8. 2dcn picpic
            automatically matched to 2DCN A:2-309
            complexed with adp, ckp, k, mg
            1. region h:2-309 [131381] picpiclink
          9. 2dcn picpic
            automatically matched to 2DCN A:2-309
            complexed with adp, ckp, k, mg
            1. region i:2-309 [131382] picpiclink
          10. 2dcn picpic
            automatically matched to 2DCN A:2-309
            complexed with adp, ckp, k, mg
            1. region j:2-309 [131383] picpiclink
          11. 2dcn picpic
            automatically matched to 2DCN A:2-309
            complexed with adp, ckp, k, mg
            1. region k:2-309 [131384] picpiclink
          12. 2dcn picpic
            automatically matched to 2DCN A:2-309
            complexed with adp, ckp, k, mg
            1. region l:2-309 [131385] picpiclink
          13. 1wye picpic
            automatically matched to 2DCN A:2-309
            1. region a:2-309 [121438] picpiclink
          14. 1wye picpic
            automatically matched to 2DCN A:2-309
            1. region b:2-309 [121439] picpiclink
          15. 1wye picpic
            automatically matched to 2DCN A:2-309
            1. region c:2-309 [121440] picpiclink
          16. 1wye picpic
            automatically matched to 2DCN A:2-309
            1. region d:2-309 [121441] picpiclink
          17. 1wye picpic
            automatically matched to 2DCN A:2-309
            1. region e:2-309 [121442] picpiclink
          18. 1wye picpic
            automatically matched to 2DCN A:2-309
            1. region f:2-309 [121443] picpiclink
    5. ADP-specific Phosphofructokinase/Glucokinase [64147] (3)
      Pfam 04587
      1. ADP-dependent glucokinase [64148]
        1. Archaeon Thermococcus litoralis [TaxId: 2265] [64149] (2)
          1. 1l2l picpic
            1. chain a [77656] picpiclink
          2. 1gc5 picpic
            complexed with adp
            1. chain a [60429] picpiclink
        2. Archaeon Pyrococcus furiosus [TaxId: 2261] [102643] (1)
          1. 1ua4 picpic
            complexed with amp, glc
            1. chain a [99128] picpiclink
      2. ADP-specific phosphofructokinase [110707]
        1. Pyrococcus horikoshii [TaxId: 53953] [110708] (1)
          SQ O59355 # PH1645
          1. 1u2x picpic
            complexed with so4
            1. chain a [107622] picpiclink
            2. chain b [107623] picpiclink
  2. MurD-like peptide ligases, catalytic domain [53623] (2)
    has extra strand located between strands 1 and 2
    link to SUPERFAMILY database - Superfamily
    1. MurCDEF [53624] (5)
      1. UDP-N-acetylmuramate-alanine ligase MurC [82520]
        1. Thermotoga maritima [TaxId: 2336] [82521] (1)
          TM0231
          1. 1j6u picpicxrefxref
            structural genomics
            complexed with mse
            1. region a:89-295 [77096] picpiclink
        2. Haemophilus influenzae [TaxId: 727] [89776] (4)
          1. 1p3d picpicxrefxref
            complexed with anp, mn, mse, uma
            1. region a:107-321 [87730] picpiclink
            2. region b:107-321 [87733] picpiclink
          2. 1p31 picpicxrefxref
            complexed with epu, mg, mse
            1. region a:107-321 [87724] picpiclink
            2. region b:107-321 [87727] picpiclink
          3. 1gqy picpicxrefxref
            complexed with acp, mg
            1. region a:107-321 [83307] picpiclink
            2. region b:107-321 [83310] picpiclink
          4. 1gqq picpicxrefxref
            1. region a:107-321 [83301] picpiclink
            2. region b:107-321 [83304] picpiclink
      2. UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD [53625]
        1. Escherichia coli [TaxId: 562] [53626] (11)
          1. 2jfg picpicxrefxref
            automatically matched to d1e0da3
            complexed with adp, so4, uma
            1. region a:94-297 [138308] picpiclink
          2. 2uag picpicxrefxref
            complexed with adp, mg, uma
            1. region a:94-297 [34954] picpiclink
          3. 4uag picpicxrefxref
            complexed with so4, uag, unx
            1. region a:94-297 [34955] picpiclink
          4. 3uag picpicxrefxref
            complexed with adp, epe, mn, uma
            1. region a:94-297 [34956] picpiclink
          5. 2jff picpicxrefxref
            automatically matched to d1e0da3
            complexed with lk2, so4
            1. region a:94-297 [138305] picpiclink
          6. 2uup picpicxrefxref
            automatically matched to d1e0da3
            complexed with lk4, so4
            1. region a:94-297 [152202] picpiclink
          7. 1uag picpicxrefxref
            complexed with so4, uma
            1. region a:94-297 [34957] picpiclink
          8. 1eeh picpicxrefxref
            complexed with uma
            1. region a:94-297 [34958] picpiclink
          9. 2jfh picpicxrefxref
            automatically matched to d1e0da3
            complexed with lk1, so4
            1. region a:94-297 [138311] picpiclink
          10. 2uuo picpicxrefxref
            automatically matched to d1e0da3
            complexed with lk3, so4
            1. region a:94-297 [152199] picpiclink
          11. 1e0d picpicxrefxref
            complexed with so4
            1. region a:94-297 [34959] picpiclink
      3. UDP-N-acetylmuramyl tripeptide synthetase MurE [64150]
        1. Escherichia coli [TaxId: 562] [64151] (1)
          1. 1e8c picpicxrefxref
            complexed with api, cl, uag
            1. region a:104-337 [59379] picpiclink
            2. region b:104-337 [59382] picpiclink
      4. UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF [53627]
        1. Escherichia coli [TaxId: 562] [53628] (1)
          1. 1gg4 picpicxrefxref
            1. region a:99-312 [58986] picpiclink
            2. region b:599-812 [58988] picpiclink
    2. Folylpolyglutamate synthetase [53629] (2)
      1. Folylpolyglutamate synthetase [53630]
        1. Lactobacillus casei [TaxId: 1582] [53631] (7)
          1. 2gc6 picpicxref
            automatically matched to d1fgs_2
            complexed with lcx, so4; mutant
            1. region a:1-296 [134953] picpiclink
          2. 2gc5 picpicxref
            automatically matched to d1fgs_2
            complexed with lcx, so4; mutant
            1. region a:1-296 [134951] picpiclink
          3. 1jbw picpicxref
            complexed with acq, mg, tmf
            1. region a:1-296 [62861] picpiclink
          4. 1jbv picpicxref
            complexed with acp, mg
            1. region a:1-296 [62859] picpiclink
          5. 2gcb picpicxref
            automatically matched to d1fgs_2
            mutant
            1. region a:1-296 [134976] picpiclink
          6. 2gca picpicxref
            automatically matched to d1fgs_2
            1. region a:1-296 [134974] picpiclink
          7. 1fgs picpicxref
            complexed with mg, pop
            1. region a:1-296 [34962] picpiclink
        2. Thermotoga maritima [TaxId: 2336] [102644] (1)
          TM0166
          1. 1o5z picpicxref
            structural genomics
            complexed with cl, so4, unl
            1. region a:-2-293 [92531] picpiclink
  3. CoaB-like [102645] (1)
    combination of the Rossmann-like and Ribokinase-like topologies; mixed beta-sheet of 8 strands, order 32145678, strand 7 is antiparallel to the rest
    link to SUPERFAMILY database - Superfamily
    1. CoaB-like [102646] (2)
      Pfam 04127
      1. Phosphopantothenoylcysteine synthetase [102647]
        1. Human (Homo sapiens) [TaxId: 9606] [102648] (1)
          1. 1p9o picpic
            complexed with so4
            1. chain a [94397] picpiclink
            2. chain b [94398] picpiclink
      2. Coenzyme A biosynthesis bifunctional protein CoaBC, phosphopantothenoylcysteine synthase domain (CoaB) [117722]
        1. Escherichia coli [TaxId: 562] [117723] (4)
          SQ P24285 181-404
          1. 1u7z picpic
            complexed with pmt; mutant
            1. chain a [113107] picpiclink
            2. chain b [113108] picpiclink
            3. chain c [113109] picpiclink
          2. 1u7w picpic
            complexed with ctp, oc2; mutant
            1. chain a [113104] picpiclink
            2. chain b [113105] picpiclink
            3. chain c [113106] picpiclink
          3. 1u7u picpic
            mutant
            1. chain a [113103] picpiclink
          4. 1u80 picpic
            complexed with c5p, po4; mutant
            1. chain a [113110] picpiclink
            2. chain b [113111] picpiclink
            3. chain c [113112] 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