Structural Classification of Proteins
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Superfamily: NagB/RpiA/CoA transferase-like

link to SUPERFAMILY database - Superfamily

Lineage:

  1. Root: scop
  2. Class: Alpha and beta proteins (a/b) [51349]
    Mainly parallel beta sheets (beta-alpha-beta units)
  3. Fold: NagB/RpiA/CoA transferase-like [100949]
    core: 3 layers: a/b/a; parallel or mixed beta-sheet of 6 strands, order 321456
  4. Superfamily: NagB/RpiA/CoA transferase-like [100950]
    link to SUPERFAMILY database - Superfamily

Families:

  1. NagB-like [52513] (3)
    share a common phosphate-binding site with the RpiA family
    1. Glucosamine 6-phosphate deaminase/isomerase NagB [52514]
      1. Escherichia coli [TaxId: 562] [52515] (10)
        1. 1fsf picpic
          1. chain a [65047] picpiclink
        2. 1jt9 picpic
          mutant
          1. chain a [67259] picpiclink
        3. 1dea picpic
          complexed with po4
          1. chain a [31760] picpiclink
          2. chain b [31761] picpiclink
        4. 1fs5 picpic
          complexed with 16g, tar
          1. chain a [65044] picpiclink
          2. chain b [65045] picpiclink
        5. 1fqo picpic
          complexed with fpc
          1. chain a [65039] picpiclink
          2. chain b [65040] picpiclink
        6. 1frz picpic
          complexed with 16g
          1. chain a [65041] picpiclink
          2. chain b [65042] picpiclink
        7. 1hot picpic
          complexed with nag, phs, po4
          1. chain a [31764] picpiclink
          2. chain b [31765] picpiclink
        8. 1cd5 picpic
          1. chain a [31766] picpiclink
        9. 1hor picpic
          complexed with agp, po4
          1. chain a [31762] picpiclink
          2. chain b [31763] picpiclink
        10. 1fs6 picpic
          1. chain a [65046] picpiclink
      2. Human (Homo sapiens) [TaxId: 9606] [102320] (1)
        1. 1ne7 picpic
          complexed with 16g, agp, glc, so4
          1. chain a [91833] picpiclink
          2. chain b [91834] picpiclink
          3. chain c [91835] picpiclink
          4. chain d [91836] picpiclink
          5. chain e [91837] picpiclink
          6. chain f [91838] picpiclink
    2. 6-phosphogluconolactonase [102321]
      1. Thermotoga maritima [TaxId: 2336] [102322] (2)
        SQ Q9X0N8 # TM1154
        1. 1vl1 picpic
          Structural genomics target
          complexed with cit
          1. chain a [108707] picpiclink
        2. 1pbt picpic
          structural genomics
          complexed with edo, fmt, so4, tmn
          1. chain a [94416] picpiclink
  2. D-ribose-5-phosphate isomerase (RpiA), catalytic domain [75176] (4)
    share a common phosphate-binding site with the NagB-like family; part of sheet is folded upon itself and forms a barrel-like structure like the CoA transferase subunits
    1. D-ribose-5-phosphate isomerase (RpiA), catalytic domain [75177]
      1. Escherichia coli [TaxId: 562] [75178] (3)
        1. 1o8b picpicxref
          complexed with abf, mse
          1. region a:23-126,a:199-218 [81180] picpiclink
          2. region b:2-126,b:199-218 [81182] picpiclink
        2. 1ks2 picpicxref
          structural genomics
          complexed with mse
          1. region a:2-126,a:199-219 [72908] picpiclink
          2. region b:2-126,b:199-219 [72910] picpiclink
        3. 1lkz picpicxref
          complexed with mse
          1. region a:1-126,a:199-219 [73991] picpiclink
          2. region b:1-126,b:199-219 [73993] picpiclink
      2. Haemophilus influenzae [TaxId: 727] [82391] (1)
        1. 1m0s picpicxref
          structural genomics
          complexed with cit
          1. region a:1-126,a:199-219 [78351] picpiclink
          2. region b:1-126,b:199-219 [78353] picpiclink
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75179] (2)
        1. 1lk5 picpicxref
          complexed with cl, na
          1. region a:1-130,a:211-229 [73960] picpiclink
          2. region b:1-130,b:211-229 [73962] picpiclink
          3. region c:1-130,c:211-229 [73964] picpiclink
          4. region d:1-130,d:211-229 [73966] picpiclink
        2. 1lk7 picpicxref
          complexed with cl, der, na
          1. region a:1-130,a:211-229 [73968] picpiclink
          2. region b:1-130,b:211-229 [73970] picpiclink
          3. region c:1-130,c:211-229 [73972] picpiclink
          4. region d:1-130,d:211-229 [73974] picpiclink
      4. Thermus thermophilus [TaxId: 274] [110512] (3)
        SQ Q72J47
        1. 1uj6 picpicxref
          complexed with a5p, cl
          1. region a:3-131,a:206-227 [107898] picpiclink
        2. 1uj4 picpicxref
          complexed with cl
          1. region a:3-131,a:206-227 [107894] picpiclink
        3. 1uj5 picpicxref
          complexed with cl, r5p
          1. region a:3-131,a:206-227 [107896] picpiclink
  3. CoA transferase beta subunit-like [74657] (3)
    catalytic subunit: similar active site structure to the NagB and RpiA families; mixed beta-sheet of 7 strands, order 4321567; strand 3 is antiparallel to the rest
    1. Glutaconate:CoA transferase beta [53320]
      1. Acidaminococcus fermentans [TaxId: 905] [53321] (1)
        1. 1poi picpicxref
          complexed with cu
          1. chain b [34155] picpiclink
          2. chain d [34156] picpiclink
    2. Succinate:CoA transferase, C-terminal domain [82466]
      1. Pig (Sus scrofa) [TaxId: 9823] [82467] (13)
        1. 1ooy picpicxref
          complexed with k, po4
          1. region a:261-481 [93388] picpiclink
          2. region b:262-481 [93390] picpiclink
        2. 1ooz picpicxref
          complexed with k; mutant
          1. region a:260-481 [93392] picpiclink
          2. region b:260-481 [93394] picpiclink
        3. 2nrc picpicxrefxrefxrefxref
          automatically matched to d1m3eb2
          mutant
          1. region a:261-480 [148370] picpiclink
        4. 2nrc picpicxrefxrefxrefxref
          automatically matched to d1m3eb2
          mutant
          1. region b:261-480 [148372] picpiclink
        5. 2nrc picpicxrefxrefxrefxref
          automatically matched to d1m3eb2
          mutant
          1. region c:261-480 [148374] picpiclink
        6. 2nrc picpicxrefxrefxrefxref
          automatically matched to d1m3eb2
          mutant
          1. region d:261-480 [148376] picpiclink
        7. 2nrb picpicxrefxrefxrefxref
          automatically matched to d1m3eb2
          complexed with cl; mutant
          1. region a:261-480 [148362] picpiclink
        8. 2nrb picpicxrefxrefxrefxref
          automatically matched to d1m3eb2
          complexed with cl; mutant
          1. region b:261-480 [148364] picpiclink
        9. 2nrb picpicxrefxrefxrefxref
          automatically matched to d1m3eb2
          complexed with cl; mutant
          1. region c:261-480 [148366] picpiclink
        10. 2nrb picpicxrefxrefxrefxref
          automatically matched to d1m3eb2
          complexed with cl; mutant
          1. region d:261-480 [148368] picpiclink
        11. 1ope picpicxref
          complexed with hg, k; mutant
          1. region a:262-481 [93400] picpiclink
          2. region b:262-481 [93402] picpiclink
        12. 1o9l picpicxref
          complexed with emc, emt
          1. region a:300-520 [81242] picpiclink
          2. region b:300-520 [81244] picpiclink
          3. region c:300-520 [81246] picpiclink
          4. region d:300-520 [81248] picpiclink
        13. 1m3e picpicxref
          complexed with mse
          1. region a:260-481 [78558] picpiclink
          2. region b:259-481 [78560] picpiclink
          3. region c:259-481 [78562] picpiclink
          4. region d:260-481 [78564] picpiclink
    3. Putative enzyme YdiF C-terminal domain [142194]
      1. Escherichia coli [TaxId: 562] [142195] (12)
        SQ P37766 283-529
        1. 2ahu picpicxrefxrefxrefxref
          1. region a:283-529 [126785] picpiclink
        2. 2ahu picpicxrefxrefxrefxref
          automatically matched to 2AHU A:283-529
          1. region b:283-529 [126787] picpiclink
        3. 2ahu picpicxrefxrefxrefxref
          automatically matched to 2AHU A:283-529
          1. region c:283-529 [126789] picpiclink
        4. 2ahu picpicxrefxrefxrefxref
          automatically matched to 2AHU A:283-529
          1. region d:283-529 [126791] picpiclink
        5. 2ahv picpicxrefxrefxrefxref
          automatically matched to 2AHU A:283-529
          complexed with coa
          1. region a:284-529 [126793] picpiclink
        6. 2ahv picpicxrefxrefxrefxref
          automatically matched to 2AHU A:283-529
          complexed with coa
          1. region b:284-529 [126795] picpiclink
        7. 2ahv picpicxrefxrefxrefxref
          automatically matched to 2AHU A:283-529
          complexed with coa
          1. region c:284-529 [126797] picpiclink
        8. 2ahv picpicxrefxrefxrefxref
          automatically matched to 2AHU A:283-529
          complexed with coa
          1. region d:284-529 [126799] picpiclink
        9. 2ahw picpicxrefxrefxrefxref
          automatically matched to 2AHU A:283-529
          complexed with coa
          1. region a:284-529 [126801] picpiclink
        10. 2ahw picpicxrefxrefxrefxref
          automatically matched to 2AHU A:283-529
          complexed with coa
          1. region b:284-529 [126803] picpiclink
        11. 2ahw picpicxrefxrefxrefxref
          automatically matched to 2AHU A:283-529
          complexed with coa
          1. region c:284-529 [126805] picpiclink
        12. 2ahw picpicxrefxrefxrefxref
          automatically matched to 2AHU A:283-529
          complexed with coa
          1. region d:284-529 [126807] picpiclink
  4. CoA transferase alpha subunit-like [74656] (6)
    parallel beta-sheet of 7 strands, order 4321567
    1. Glutaconate:CoA transferase alpha [53318]
      1. Acidaminococcus fermentans [TaxId: 905] [53319] (1)
        1. 1poi picpicxref
          complexed with cu
          1. chain a [34153] picpiclink
          2. chain c [34154] picpiclink
    2. Acetate:CoA transferase alpha [75257]
      1. Escherichia coli [TaxId: 562] [75258] (1)
        1. 1k6d picpic
          complexed with mg
          1. chain a [72082] picpiclink
          2. chain b [72083] picpiclink
    3. Succinate:CoA transferase, N-terminal domain [82464]
      1. Pig (Sus scrofa) [TaxId: 9823] [82465] (13)
        1. 1ooy picpicxref
          complexed with k, po4
          1. region a:1-242 [93389] picpiclink
          2. region b:1-248 [93391] picpiclink
        2. 1ooz picpicxref
          complexed with k; mutant
          1. region a:1-246 [93393] picpiclink
          2. region b:1-246 [93395] picpiclink
        3. 2nrc picpicxrefxrefxrefxref
          automatically matched to d1m3ea1
          mutant
          1. region a:1-247 [148371] picpiclink
        4. 2nrc picpicxrefxrefxrefxref
          automatically matched to d1m3ea1
          mutant
          1. region b:1-247 [148373] picpiclink
        5. 2nrc picpicxrefxrefxrefxref
          automatically matched to d1m3ea1
          mutant
          1. region c:1-247 [148375] picpiclink
        6. 2nrc picpicxrefxrefxrefxref
          automatically matched to d1m3ea1
          mutant
          1. region d:1-247 [148377] picpiclink
        7. 2nrb picpicxrefxrefxrefxref
          automatically matched to d1m3ea1
          complexed with cl; mutant
          1. region a:1-247 [148363] picpiclink
        8. 2nrb picpicxrefxrefxrefxref
          automatically matched to d1m3ea1
          complexed with cl; mutant
          1. region b:1-247 [148365] picpiclink
        9. 2nrb picpicxrefxrefxrefxref
          automatically matched to d1m3ea1
          complexed with cl; mutant
          1. region c:1-247 [148367] picpiclink
        10. 2nrb picpicxrefxrefxrefxref
          automatically matched to d1m3ea1
          complexed with cl; mutant
          1. region d:1-247 [148369] picpiclink
        11. 1ope picpicxref
          complexed with hg, k; mutant
          1. region a:1-246 [93401] picpiclink
          2. region b:1-246 [93403] picpiclink
        12. 1o9l picpicxref
          complexed with emc, emt
          1. region a:40-286 [81241] picpiclink
          2. region b:40-286 [81243] picpiclink
          3. region c:40-285 [81245] picpiclink
          4. region d:40-282 [81247] picpiclink
        13. 1m3e picpicxref
          complexed with mse
          1. region a:1-250 [78557] picpiclink
          2. region b:1-250 [78559] picpiclink
          3. region c:1-250 [78561] picpiclink
          4. region d:1-250 [78563] picpiclink
    4. Putative citrate lyase alpha chain, citF2 [117515]
      duplication: consists of two topologically similar domains
      1. Salmonella typhimurium [TaxId: 90371] [117516] (1)
        SQ Q8ZRY1
        1. 1xr4 picpic
          Structural genomics target
          1. region a:1-236 [115860] picpiclink
          2. region a:237-505 [115861] picpiclink
          3. region b:1-236 [115862] picpiclink
          4. region b:237-505 [115863] picpiclink
    5. Acetyl-CoA hydrolase (PA5445) [142196]
      duplication: consists of two topologically similar domains; overall similarity to CitF2
      1. Pseudomonas aeruginosa [TaxId: 287] [142197] (4)
        SQ Q9HTC2 224-497! SQ Q9HTC2 3-223
        1. 2g39 picpic
          complexed with acy, edo
          1. region a:3-223 [134553] picpiclink
        2. 2g39 picpic
          complexed with acy, edo
          1. region a:224-497 [134554] picpiclink
        3. 2g39 picpic
          automatically matched to 2G39 A:3-223
          complexed with acy, edo
          1. region b:4-223 [134555] picpiclink
        4. 2g39 picpic
          automatically matched to 2G39 A:224-497
          complexed with acy, edo
          1. region b:224-497 [134556] picpiclink
    6. Putative enzyme YdiF N-terminal domain [142198]
      1. Escherichia coli [TaxId: 562] [142199] (12)
        SQ P37766 4-276
        1. 2ahu picpicxrefxrefxrefxref
          1. region a:4-276 [126786] picpiclink
        2. 2ahu picpicxrefxrefxrefxref
          automatically matched to 2AHU A:4-276
          1. region b:4-276 [126788] picpiclink
        3. 2ahu picpicxrefxrefxrefxref
          automatically matched to 2AHU A:4-276
          1. region c:4-276 [126790] picpiclink
        4. 2ahu picpicxrefxrefxrefxref
          automatically matched to 2AHU A:4-276
          1. region d:4-276 [126792] picpiclink
        5. 2ahv picpicxrefxrefxrefxref
          automatically matched to 2AHU A:4-276
          complexed with coa
          1. region a:4-276 [126794] picpiclink
        6. 2ahv picpicxrefxrefxrefxref
          automatically matched to 2AHU A:4-276
          complexed with coa
          1. region b:4-276 [126796] picpiclink
        7. 2ahv picpicxrefxrefxrefxref
          automatically matched to 2AHU A:4-276
          complexed with coa
          1. region c:4-276 [126798] picpiclink
        8. 2ahv picpicxrefxrefxrefxref
          automatically matched to 2AHU A:4-276
          complexed with coa
          1. region d:4-276 [126800] picpiclink
        9. 2ahw picpicxrefxrefxrefxref
          automatically matched to 2AHU A:4-276
          complexed with coa
          1. region a:4-276 [126802] picpiclink
        10. 2ahw picpicxrefxrefxrefxref
          automatically matched to 2AHU A:4-276
          complexed with coa
          1. region b:4-276 [126804] picpiclink
        11. 2ahw picpicxrefxrefxrefxref
          automatically matched to 2AHU A:4-276
          complexed with coa
          1. region c:4-276 [126806] picpiclink
        12. 2ahw picpicxrefxrefxrefxref
          automatically matched to 2AHU A:4-276
          complexed with coa
          1. region d:4-276 [126808] picpiclink
  5. IF2B-like [110513] (5)
    Pfam 01008; contains extra N-terminal alpha+beta domain (1-126); beta(3)-alpha(5); 3 layers: b/a/a
    1. Probable methylthioribose-1-phosphate isomerase TM0911 [110514]
      1. Thermotoga maritima [TaxId: 2336] [110515] (1)
        SQ Q9X013
        1. 1t9k picpic
          Structural genomics target
          complexed with cl, so4
          1. chain a [106721] picpiclink
          2. chain b [106722] picpiclink
          3. chain c [106723] picpiclink
          4. chain d [106724] picpiclink
    2. Putative methylthioribose-1-phosphate isomerase Ypr118W [110516]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110517] (1)
        SQ Q06489
        1. 1w2w picpic
          complexed with so4
          1. chain a,b [109130] picpiclink
          2. chain e,f [109131] picpiclink
          3. chain i,j [109132] picpiclink
          4. chain m,n [109133] picpiclink
    3. Putative eIF-2B delta-subunit [110518]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [110519] (1)
        SQ O29877 # AF0370
        1. 1t5o picpic
          1. chain a [106459] picpiclink
          2. chain b [106460] picpiclink
          3. chain c [106461] picpiclink
          4. chain d [106462] picpiclink
    4. Putative eIF-2B subunit 2-like protein PH0440 [117517]
      1. Pyrococcus horikoshii [TaxId: 53953] [117518] (1)
        SQ O58185
        1. 1vb5 picpic
          1. chain a [113604] picpiclink
          2. chain b [113605] picpiclink
    5. Initiation factor 2b [159543]
      1. Leishmania major [TaxId: 5664] [159544] (2)
        SQ Q4Q0R9 133-506,133-506
        1. 2a0u picpic
          complexed with so4
          1. region a:10-383 [146036] picpiclink
        2. 2a0u picpic
          automatically matched to 2A0U A:10-383
          complexed with so4
          1. region b:17-383 [146037] picpiclink
  6. Methenyltetrahydrofolate synthetase [110520] (3)
    Pfam 01812; 5-FTHF cyclo-ligase
    1. Hypothetical protein aq_1731 [110521]
      1. Aquifex aeolicus [TaxId: 63363] [110522] (1)
        SQ O67621
        1. 1sou picpic
          Structural genomics target
          1. chain a [105858] picpiclink
    2. 5,10-methenyltetrahydrofolate synthetase homolog MPN348 [110523]
      1. Mycoplasma pneumoniae [TaxId: 2104] [110524] (3)
        SQ P75430
        1. 1sbq picpic
          Structural genomics target
          complexed with so4
          1. chain a [105412] picpiclink
          2. chain b [105413] picpiclink
        2. 1u3f picpic
          Structural genomics target
          complexed with adp, mg, po4
          1. chain a [112997] picpiclink
          2. chain b [112998] picpiclink
        3. 1u3g picpic
          Structural genomics target
          complexed with adp, mg, po4, thf
          1. chain a [112999] picpiclink
    3. Hypothetical protein TTHA1611 [117519]
      1. Thermus thermophilus [TaxId: 274] [117520] (1)
        SQ Q5SHW9 1-175
        1. 1wkc picpic
          Structural genomics target
          complexed with so4
          1. chain a [114724] picpiclink
  7. YkgG-like [142200] (1)
    Pfam 02589; DUF162
    1. Hypothetical protein DR1909 [142201]
      1. Deinococcus radiodurans [TaxId: 1299] [142202] (1)
        SQ Q9RT57 38-212
        1. 2g40 picpic
          1. region a:38-212 [134575] picpiclink
  8. SorC sugar-binding domain-like [159545] (5)
    Pfam 04198
    1. Transcriptional regulator PSPTO2395 [159546]
      1. Pseudomonas syringae [TaxId: 317] [159547] (1)
        SQ Q883G8 59-316
        1. 2r5f picpic
          complexed with so4
          1. region a:59-316 [151590] picpiclink
    2. Transcriptional regulator SP0247 [159548]
      1. Streptococcus pneumoniae [TaxId: 1313] [159549] (1)
        SQ Q97SS7 56-317
        1. 2gnp picpic
          complexed with peg
          1. region a:56-317 [147139] picpiclink
    3. Transcriptional regulator EF1965 [159550]
      1. Enterococcus faecalis [TaxId: 1351] [159551] (1)
        SQ Q833I7 95-341
        1. 2o0m picpic
          complexed with po4
          1. region a:95-341 [148543] picpiclink
    4. Sor-operon regulator SorC [159552]
      1. Shigella flexneri [TaxId: 623] [159553] (4)
        SQ Q83PA8 61-315
        1. 3efb picpic
          complexed with acy
          1. region a:11-265 [158129] picpiclink
        2. 3efb picpic
          automatically matched to 3EFB A:11-265
          complexed with acy
          1. region b:11-265 [158130] picpiclink
        3. 3efb picpic
          automatically matched to 3EFB A:11-265
          complexed with acy
          1. region c:11-264 [158131] picpiclink
        4. 3efb picpic
          automatically matched to 3EFB A:11-265
          complexed with acy
          1. region d:11-265 [158132] picpiclink
    5. Central glycolytic gene regulator CggR [159554]
      formerly hypothetical protein YvbQ
      1. Bacillus subtilis [TaxId: 1423] [159555] (10)
        SQ O32253 89-338
        1. 2okg picpic
          complexed with cl, g3h
          1. region a:89-338 [148805] picpiclink
        2. 2okg picpic
          automatically matched to 2OKG A:89-338
          complexed with cl, g3h
          1. region b:89-338 [148806] picpiclink
        3. 3bxe picpic
          automatically matched to 2OKG A:89-338
          complexed with 13p
          1. region a:93-338 [155708] picpiclink
        4. 3bxe picpic
          automatically matched to 2OKG A:89-338
          complexed with 13p
          1. region b:89-338 [155709] picpiclink
        5. 3bxh picpic
          automatically matched to 2OKG A:89-338
          complexed with f6p, scn
          1. region a:93-338 [155714] picpiclink
        6. 3bxh picpic
          automatically matched to 2OKG A:89-338
          complexed with f6p, scn
          1. region b:89-338 [155715] picpiclink
        7. 3bxf picpic
          automatically matched to 2OKG A:89-338
          complexed with 13p, cl, fbp
          1. region a:89-338 [155710] picpiclink
        8. 3bxf picpic
          automatically matched to 2OKG A:89-338
          complexed with 13p, cl, fbp
          1. region b:94-338 [155711] picpiclink
        9. 3bxg picpic
          automatically matched to 2OKG A:89-338
          complexed with bg6
          1. region a:93-338 [155712] picpiclink
        10. 3bxg picpic
          automatically matched to 2OKG A:89-338
          complexed with bg6
          1. region b:89-338 [155713] picpiclink
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