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

core: 3 layers: a/b/a; parallel or mixed beta-sheet of 6 strands, order 321456

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

Superfamilies:

  1. NagB/RpiA/CoA transferase-like [100950] (8)
    link to SUPERFAMILY database - Superfamily
    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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