Structural Classification of Proteins

Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like

: the constituent families form similar dimers
uperfamily

Lineage:

Root: scop
Class: Alpha and beta proteins (a/b) [51349]
Mainly parallel beta sheets (beta-alpha-beta units)
Fold: Isocitrate/Isopropylmalate dehydrogenase-like [53658]
consists of two intertwined (sub)domains related by pseudo dyad; duplication
3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213A945867 (A=10); strands from 5 to 9 are antiparallel to the rest
Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like [53659]
the constituent families form similar dimers
uperfamily

Families:

Dimeric isocitrate & isopropylmalate dehydrogenases [53660] (13)
the active site is between the two identical subunits
1. 3-isopropylmalate dehydrogenase, IPMDH [53661]
  1. Thermus thermophilus [TaxId: 274] [53662] (14)
    1. 1xaa
      1. chain a [35033]
    2. 1g2u
      mutant
      1. chain a [35036]
    3. 1xab
      1. chain a [35034]
    4. 1idm
      mutant
      1. chain a [35035]
    5. 1gc9
      mutant
      1. chain a [35037]
    6. 1osj
      mutant
      1. chain a [35039]
      2. chain b [35040]
    7. 1wal
      mutant
      1. chain a [35041]
    8. 1hex
      complexed with nad
      1. chain a [35044]
    9. 1gc8
      mutant
      1. chain a [35042]
      2. chain b [35043]
    10. 1ipd
      complexed with so4
      1. chain a [35038]
    11. 1osi
      1. chain a [35047]
      2. chain b [35048]
      3. chain c [35049]
      4. chain d [35050]
    12. 1dr0
      1. chain a [35045]
      2. chain b [35046]
    13. 1dr8
      1. chain a [35051]
      2. chain b [35052]
    14. 1dpz
      1. chain a [35053]
      2. chain b [35054]
  2. Chimera (Thermus thermophilus) and (Bacillus subtilis) [TaxId: 274] [53663] (2)
    1. 1xad
      mutant
      1. chain a [35055]
    2. 1xac
      mutant
      1. chain a [35056]
  3. Bacillus coagulans [TaxId: 1398] [53664] (3)
    1. 2ayq
      1. chain a [35057]
      2. chain b [35058]
    2. 1v53
      automatically matched to d2ayqb_
      1. region a:1-356 [119836]
    3. 1v53
      automatically matched to d2ayqb_
      1. region b:1-356 [119837]
  4. Thiobacillus ferrooxidans [TaxId: 920] [53665] (1)
    1. 1a05
      complexed with ipm, mg
      1. chain a [35059]
      2. chain b [35060]
  5. Salmonella typhimurium [TaxId: 90371] [53666] (1)
    1. 1cnz
      complexed with mn, so4
      1. chain a [35061]
      2. chain b [35062]
  6. Escherichia coli [TaxId: 562] [53667] (1)
    1. 1cm7
      1. chain a [35063]
      2. chain b [35064]
  7. Thermotoga maritima [TaxId: 2336] [110714] (1)
    SQ Q9WZ26
    1. 1vlc
      Structural genomics target
      complexed with cl
      1. chain a [108743]
  8. Sulfolobus tokodaii [TaxId: 111955] [117724] (1)
    SQ P50455
    1. 1wpw
      complexed with mg
      1. chain a [114830]
      2. chain b [114831]
  9. Mycobacterium tuberculosis [TaxId: 1773] [117725] (5)
    SQ P95313
    1. 1w0d
      complexed with so4
      1. chain a [114060]
      2. chain b [114061]
      3. chain c [114062]
      4. chain d [114063]
    2. 2g4o
      automatically matched to d1w0da_
      complexed with cl, so4
      1. region a:1-336 [134604]
    3. 2g4o
      automatically matched to d1w0da_
      complexed with cl, so4
      1. region b:1-336 [134605]
    4. 2g4o
      automatically matched to d1w0da_
      complexed with cl, so4
      1. region c:1-336 [134606]
    5. 2g4o
      automatically matched to d1w0da_
      complexed with cl, so4
      1. region d:1-336 [134607]
2. Isocitrate dehydrogenase, ICDH [53668]
  1. Escherichia coli [TaxId: 562] [53669] (26)
    1. 1pb1
      complexed with gol, ici, so4
      1. chain a [88014]
    2. 1pb3
      complexed with gol, so4
      1. chain a [88015]
    3. 1iso
      complexed with nad, so4; mutant
      1. chain a [35065]
    4. 1ai3
      complexed with itm, ndo
      1. chain a [35066]
    5. 1ai2
      complexed with ica, nap
      1. chain a [35067]
    6. 1p8f
      complexed with gol, ici, mg, so4
      1. chain a [87943]
    7. 1cw4
      complexed with akg, mn, so4; mutant
      1. chain a [35068]
    8. 1cw1
      complexed with ici, mn, so4; mutant
      1. chain a [35069]
    9. 1sjs
      1. chain a [35071]
    10. 1hj6
      complexed with gol, ipm, mg, nap; mutant
      1. chain a [35070]
    11. 1cw7
      complexed with ici, mg, so4
      1. chain a [35087]
    12. 7icd
      mutant
      1. chain a [35072]
    13. 1grp
      complexed with ict, mg; mutant
      1. chain a [35077]
    14. 9icd
      complexed with nap
      1. chain a [35075]
    15. 8icd
      complexed with ict, mg; mutant
      1. chain a [35076]
    16. 4icd
      complexed with pho
      1. chain a [35074]
    17. 1gro
      complexed with ict, mg; mutant
      1. chain a [35079]
    18. 3icd
      1. chain a [35078]
    19. 5icd
      complexed with ict, mg
      1. chain a [35080]
    20. 1idc
      complexed with mg, oxs; mutant
      1. chain a [35073]
    21. 6icd
      mutant
      1. chain a [35081]
    22. 1bl5
      complexed with akg, mg, nap
      1. chain a [35083]
    23. 1idd
      mutant
      1. chain a [35084]
    24. 1ide
      complexed with ict, mg, nap; mutant
      1. chain a [35082]
    25. 1idf
      mutant
      1. chain a [35086]
    26. 1ika
      complexed with akg, ca
      1. chain a [35085]
  2. Bacillus subtilis [TaxId: 1423] [64171] (1)
    1. 1hqs
      complexed with cit, pgq, pgr
      1. chain a [61154]
      2. chain b [61155]
3. NADP-dependent isocitrate dehydrogenase [82524]
  1. Pig (Sus scrofa) [TaxId: 9823] [82525] (2)
    1. 1lwd
      complexed with ict, mn, so4
      1. chain a [78265]
      2. chain b [78266]
    2. 1j1w
      complexed with nap
      1. chain a [90772]
      2. chain b [90773]
      3. chain c [90774]
      4. chain d [90775]
  2. Human (Homo sapiens) [TaxId: 9606] [110715] (2)
    SQ O75874
    1. 1t0l
      complexed with ca, ict, nap
      1. chain a [106216]
      2. chain b [106217]
      3. chain c [106218]
      4. chain d [106219]
    2. 1t09
      complexed with nap
      1. chain a [106197]
      2. chain b [106198]
PdxA-like [102656] (2)
Pfam 04166; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PlsX-like and phosphotransacetylase families
1. 4-hydroxythreonine-4-phosphate dehydrogenase PdxA [102657]
  pyridoxal phosphate biosynthetic protein
  1. Escherichia coli [TaxId: 562] [102658] (3)
    1. 1ptm
      complexed with po4, zn
      1. chain a [95104]
      2. chain b [95105]
    2. 1ps6
      complexed with 4tp, zn
      1. chain a [95070]
      2. chain b [95071]
    3. 1ps7
      complexed with zn
      1. chain a [95072]
      2. chain b [95073]
      3. chain c [95074]
      4. chain d [95075]
  2. Salmonella typhimurium [TaxId: 90371] [102659] (1)
    1. 1r8k
      complexed with cl, co, so4
      1. chain a [97240]
      2. chain b [97241]
PlsX-like [102660] (2)
Pfam 02504; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PdxA-like and phosphotransacetylase families
1. Fatty acid/phospholipid synthesis protein PlsX [102661]
  1. Bacillus subtilis [TaxId: 1423] [102662] (1)
    1. 1vi1
      structural genomics
      1. chain a [100724]
      2. chain b [100725]
  2. Enterococcus faecalis [TaxId: 1351] [110716] (1)
    SQ Q82ZE8
    1. 1u7n
      Structural genomics target
      complexed with edo, eoh
      1. chain a [107726]
      2. chain b [107727]
Phosphotransacetylase [102663] (4)
Pfam 01515; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PdxA-like and PlsX-like families
1. Phosphotransacetylase Pta [110717]
  1. Methanosarcina thermophila [TaxId: 2210] [110718] (5)
    SQ P38503
    1. 2af4
      automatically matched to d1qzta_
      complexed with coa
      1. region c:2-333 [126656]
    2. 2af4
      automatically matched to d1qzta_
      complexed with coa
      1. region d:2-332 [126657]
    3. 1qzt
      complexed with so4
      1. chain a [104670]
      2. chain b [104671]
      3. chain c [104672]
      4. chain d [104673]
    4. 2af3
      automatically matched to d1qzta_
      complexed with coa, so4
      1. region c:2-333 [126654]
    5. 2af3
      automatically matched to d1qzta_
      complexed with coa, so4
      1. region d:2-333 [126655]
  2. Streptococcus pyogenes [TaxId: 1314] [102665] (1)
    1. 1r5j
      structural genomics
      1. chain a [97097]
      2. chain b [97098]
  3. Bacillus subtilis [TaxId: 1423] [117726] (2)
    SQ P39646
    1. 1xco
      Structural genomics target
      complexed with so4, uvw
      1. chain a [115128]
      2. chain b [115129]
      3. chain c [115130]
      4. chain d [115131]
      5. chain e [115132]
      6. chain f [115133]
    2. 1td9
      Structural genomics target
      complexed with so4
      1. chain a [112391]
      2. chain b [112392]
      3. chain c [112393]
      4. chain d [112394]
      5. chain e [112395]
      6. chain f [112396]
2. Ethanolamine utilization protein EutD [117727]
  1. Escherichia coli [TaxId: 562] [117728] (1)
    SQ P77218 2-323
    1. 1vmi
      Structural genomics target
      complexed with gol
      1. chain a [113678]
Monomeric isocitrate dehydrogenase [82526] (1)
the active site is contained within one subunit between the canonical ICDH fold and a large insert domain that itself is a probable rudiment form of ICDH fold resulted from duplication, domain swapping and deletion
1. Monomeric isocitrate dehydrogenase [82527]
  1. Azotobacter vinelandii [TaxId: 354] [82528] (1)
    the insert region spans residues 150-404
    1. 1itw
      complexed with ici, mn
      1. chain a [76793]
      2. chain b [76794]
      3. chain c [76795]
      4. chain d [76796]