Structural Classification of Proteins

Superfamily: PLP-binding barrel

: circular permutation of the canonical fold: begins with an alpha helix and ends with a beta-strand
uperfamily

Lineage:

Root: scop
Class: Alpha and beta proteins (a/b) [51349]
Mainly parallel beta sheets (beta-alpha-beta units)
Fold: TIM beta/alpha-barrel [51350]
contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
the first seven superfamilies have similar phosphate-binding sites
Superfamily: PLP-binding barrel [51419]
circular permutation of the canonical fold: begins with an alpha helix and ends with a beta-strand
uperfamily

Families:

Alanine racemase-like, N-terminal domain [51420] (9)
1. Alanine racemase [51421]
  1. Bacillus stearothermophilus [TaxId: 1422] [51422] (8)
    1. 1bd0
      complexed with in5
      1. region a:12-244 [28642]
      2. region b:12-244 [28643]
    2. 1sft
      complexed with act, plp
      1. region a:12-244 [28644]
      2. region b:12-244 [28645]
    3. 1l6f
      complexed with kcx, pdl
      1. region a:12-244 [73610]
      2. region b:12-244 [73612]
    4. 1l6g
      complexed with kcx, pdd
      1. region a:12-244 [73614]
      2. region b:12-244 [73616]
    5. 2sfp
      complexed with plp, ppi
      1. region a:12-244 [28646]
      2. region b:12-244 [28647]
    6. 1ftx
      complexed with in5, kcx
      1. region a:12-244 [76192]
      2. region b:12-244 [76194]
    7. 1niu
      complexed with scp
      1. region a:12-244 [91894]
      2. region b:12-244 [91896]
    8. 1epv
      complexed with kcx, scp
      1. region a:12-244 [76147]
      2. region b:12-244 [76149]
  2. Pseudomonas aeruginosa [TaxId: 287] [110345] (1)
    SQ Q9HTQ2
    1. 1rcq
      complexed with plp
      1. region a:8-233 [104883]
  3. Streptomyces lavendulae [TaxId: 1914] [110346] (3)
    SQ Q65YW7
    1. 1vfs
      complexed with cl, scp
      1. region a:13-249 [108585]
      2. region b:1013-1249 [108587]
    2. 1vfh
      complexed with plp
      1. region a:13-249 [108575]
    3. 1vft
      complexed with cl, scp
      1. region a:13-249 [108589]
      2. region b:1013-1249 [108591]
2. Eukaryotic ornithine decarboxylase [51423]
  1. Human (Homo sapiens) [TaxId: 9606] [51424] (1)
    1. 1d7k
      1. region a:44-283 [28648]
      2. region b:44-283 [28649]
  2. Mouse (Mus musculus) [TaxId: 10090] [51425] (1)
    1. 7odc
      complexed with plp; mutant
      1. region a:44-283 [28650]
  3. Trypanosoma brucei [TaxId: 5691] [51426] (5)
    SQ P07805
    1. 2tod
      1. region a:44-283 [28651]
      2. region b:44-283 [28652]
      3. region c:44-283 [28653]
      4. region d:44-283 [28654]
    2. 1f3t
      complexed with plp, put
      1. region a:44-283 [28655]
      2. region b:44-283 [28656]
      3. region c:44-283 [28657]
      4. region d:44-283 [28658]
    3. 1szr
      complexed with orx, plg, pxp; mutant
      1. region a:44-283 [112175]
      2. region b:44-283 [112177]
      3. region c:44-283 [112179]
      4. region d:44-283 [112181]
    4. 1njj
      complexed with get, orx
      1. region a:44-283 [91906]
      2. region b:44-283 [91908]
      3. region c:44-283 [91910]
      4. region d:44-283 [91912]
    5. 1qu4
      1. region a:44-283 [28659]
      2. region b:44-283 [28660]
      3. region c:44-283 [28661]
      4. region d:44-283 [28662]
3. Diaminopimelate decarboxylase LysA [89457]
  most similar to eukaryotic ODC
  1. Mycobacterium tuberculosis [TaxId: 1773] [89458] (2)
    1. 1hkv
      complexed with lys, plp
      1. region a:46-310 [83560]
      2. region b:46-310 [83562]
    2. 1hkw
      complexed with mse, so4
      1. region a:46-310 [83564]
      2. region b:46-310 [83566]
  2. Escherichia coli [TaxId: 562] [102048] (2)
    1. 1knw
      complexed with li, mes, plp, sul
      1. region a:32-278 [90970]
    2. 1ko0
      complexed with lys, plp
      1. region a:32-278 [90972]
  3. Archaeon Methanococcus jannaschii [TaxId: 2190] [110347] (2)
    SQ Q58497
    1. 1twi
      Structural genomics target
      complexed with lys, mg, plp
      1. region a:50-313 [107400]
      2. region b:50-313 [107402]
      3. region c:50-313 [107404]
      4. region d:50-313 [107406]
    2. 1tuf
      Structural genomics target
      complexed with az1
      1. region a:50-313 [107336]
      2. region b:50-313 [107338]
"Hypothetical" protein ybl036c [51427] (1)
1. "Hypothetical" protein ybl036c [51428]
  structure from BNL's human proteome project
  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51429] (2)
    1. 1ct5
      complexed with plp
      1. chain a [28663]
    2. 1b54
      complexed with plp
      1. chain a [28664]