Structural Classification of Proteins

Superfamily: Class I glutamine amidotransferase-like

: conserved positions of the oxyanion hole and catalytic nucleophile; different constituent families contain different additional structures
uperfamily

Lineage:

Root: scop
Class: Alpha and beta proteins (a/b) [51349]
Mainly parallel beta sheets (beta-alpha-beta units)
Fold: Flavodoxin-like [52171]
3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345
Superfamily: Class I glutamine amidotransferase-like [52317]
conserved positions of the oxyanion hole and catalytic nucleophile; different constituent families contain different additional structures
uperfamily

Families:

Class I glutamine amidotransferases (GAT) [52318] (18)
contains a catalytic Cys-His-Glu triad
1. GMP synthetase [52319]
  1. Escherichia coli [TaxId: 562] [52320] (1)
    1. 1gpm
      complexed with amp, cit, mg, po4, pop
      1. region a:3-207 [31405]
      2. region b:3-207 [31406]
      3. region c:3-207 [31407]
      4. region d:3-207 [31408]
2. Carbamoyl phosphate synthetase, small subunit C-terminal domain [52321]
  1. Escherichia coli [TaxId: 562] [52322] (10)
    SQ P00907
    1. 1a9x
      complexed with adp, cl, k, mn, net, orn, po4; mutant
      1. region b:1653-1880 [31409]
      2. region d:3653-3880 [31410]
      3. region f:5653-5880 [31411]
      4. region h:7653-7880 [31412]
    2. 1c30
      1. region b:153-380 [31413]
      2. region d:153-380 [31414]
      3. region f:153-380 [31415]
      4. region h:153-380 [31416]
    3. 1cs0
      1. region b:153-380 [31417]
      2. region d:153-380 [31418]
      3. region f:153-380 [31419]
      4. region h:153-380 [31420]
    4. 1t36
      complexed with adp, cl, k, mn, net, orn, po4, u; mutant
      1. region b:153-380 [106308]
      2. region d:153-380 [106316]
      3. region f:153-380 [106324]
      4. region h:153-380 [106332]
    5. 1jdb
      complexed with adp, cl, e4n, k, mn, orn, po4
      1. region c:153-380 [31433]
      2. region f:153-381 [31434]
      3. region i:153-380 [31435]
      4. region l:153-380 [31436]
    6. 1kee
      complexed with 143, adp, cl, k, mn, net, orn, pi
      1. region b:153-380 [68499]
      2. region d:153-380 [68507]
      3. region f:153-380 [68515]
      4. region h:153-380 [68523]
    7. 1m6v
      complexed with adp, cl, k, mn, net, orn, pi; mutant
      1. region b:153-380 [74543]
      2. region d:153-380 [74551]
      3. region f:153-380 [74559]
      4. region h:153-380 [74567]
    8. 1c3o
      1. region b:153-380 [31421]
      2. region d:153-380 [31422]
      3. region f:153-380 [31423]
      4. region h:153-380 [31424]
    9. 1ce8
      complexed with adp, cl, imp, k, mn, net, orn, pi
      1. region b:153-380 [31425]
      2. region d:153-380 [31426]
      3. region f:153-380 [31427]
      4. region h:153-380 [31428]
    10. 1bxr
      complexed with anp, cl, k, mn, net, orn
      1. region b:153-380 [31429]
      2. region d:153-380 [31430]
      3. region f:153-380 [31431]
      4. region h:153-380 [31432]
3. Anthranilate synthase GAT subunit, TrpG [52323]
  1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [52324] (1)
    1. 1qdl
      1. chain b [31437]
  2. Salmonella typhimurium [TaxId: 90371] [63969] (1)
    1. 1i1q
      complexed with trp
      1. chain b [61544]
  3. Serratia marcescens [TaxId: 615] [63970] (2)
    1. 1i7q
      complexed with bez, ilg, mg, pyr
      1. chain b [61902]
      2. chain d [61904]
    2. 1i7s
      complexed with trp
      1. chain b [61906]
      2. chain d [61908]
4. GAT subunit, HisH, (or domain) of imidazoleglycerolphosphate synthase HisF [69447]
  1. Thermotoga maritima [TaxId: 2336] [69448] (3)
    1. 1k9v
      complexed with acy
      1. chain f [68365]
    2. 1gpw
      complexed with po4; mutant
      1. chain b [65461]
      2. chain d [65463]
      3. chain f [65465]
    3. 1kxj
      complexed with po4
      1. chain a [73153]
      2. chain b [73154]
  2. Thermus thermophilus [TaxId: 274] [82350] (1)
    1. 1ka9
      1. chain h [77308]
  3. Baker's yeast (Saccharomyces cerevisiae), His7 [TaxId: 4932] [69449] (4)
    1. 1jvn
      complexed with 143, ni, pop, so4
      1. region a:-3-229 [67356]
      2. region b:-3-229 [67358]
    2. 1ox6
      complexed with ni, pop, so4
      1. region a:-3-229 [87506]
      2. region b:-3-229 [87508]
    3. 1ox5
      complexed with 1pr, 5cs, ni; mutant
      1. region a:-3-229 [87502]
      2. region b:3-229 [87504]
    4. 1ox4
      complexed with cyd, ni, pop, so4
      1. region a:-3-229 [87498]
      2. region b:-3-229 [87500]
5. gamma-glutamyl hydrolase [75154]
  1. Human (Homo sapiens) [TaxId: 9606] [75155] (1)
    1. 1l9x
      complexed with bme
      1. chain a [73762]
      2. chain b [73763]
      3. chain c [73764]
      4. chain d [73765]
6. Hypothetical protein TM1158 [89599]
  1. Thermotoga maritima [TaxId: 2336] [89600] (1)
    1. 1o1y
      structural genomics
      complexed with mse, ocs, so4
      1. chain a [86554]
7. Hypothetical protein YaaE [102250]
  glutamine amidotransferase of SNO/PDX2 family implicated in pyridoxine biosynthesis
  1. Bacillus subtilis [TaxId: 1423] [102251] (3)
    1. 2nv0
      automatically matched to d1r9ga_
      1. region a:1-195 [138625]
    2. 2nv0
      automatically matched to d1r9ga_
      1. region b:1-194 [138626]
    3. 1r9g
      1. chain a [97258]
      2. chain b [97259]
  2. Bacillus stearothermophilus [TaxId: 1422] [102252] (1)
    1. 1q7r
      structural genomics
      complexed with cl, edo, so4
      1. chain a [96054]
8. CTP synthase PyrG, C-terminal domain [110481]
  1. Escherichia coli [TaxId: 562] [110482] (1)
    SQ P08398
    1. 1s1m
      complexed with iod, mg, mpd, so4
      1. region a:287-544 [105201]
      2. region b:287-545 [105203]
  2. Thermus thermophilus [TaxId: 274] [110483] (3)
    SQ Q5SIA8
    1. 1vco
      complexed with gln
      1. region a:298-547 [108508]
    2. 1vcm
      1. region a:298-547 [108504]
    3. 1vcn
      complexed with so4
      1. region a:298-547 [108506]
9. FGAM synthase PurL, amidotransferase domain [110484]
  1. Salmonella typhimurium [TaxId: 90371] [110485] (1)
    SQ P74881
    1. 1t3t
      complexed with adp, mg, so4
      1. region a:1034-1295 [106382]
10. GMP synthase subunit A, GuaAA [142065]
  1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [142066] (4)
    SQ Q9HJM3 1-196
    1. 2a9v
      complexed with cl, gol, scn
      1. region a:1-196 [126452]
    2. 2a9v
      automatically matched to 2A9V A:1-196
      complexed with cl, gol, scn
      1. region b:1-196 [126453]
    3. 2a9v
      automatically matched to 2A9V A:1-196
      complexed with cl, gol, scn
      1. region c:1-196 [126454]
    4. 2a9v
      automatically matched to 2A9V A:1-196
      complexed with cl, gol, scn
      1. region d:1-196 [126455]
  2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142067] (1)
    SQ O59071 1-188
    1. 1wl8
      complexed with acy, cl, snn
      1. region a:1-188 [120997]
11. Pyridoxine biosynthesis protein 2, Pdx2 [142068]
  1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [142069] (2)
    SQ Q5ND68 2-219
    1. 2abw
      complexed with pg4
      1. region a:2-219 [126535]
    2. 2abw
      automatically matched to 2ABW A:2-219
      complexed with pg4
      1. region b:2-219 [126536]
A4 beta-galactosidase middle domain [82351] (1)
probable non-catalytic branch of the class I GAT family; overall fold is very similar but the active site is not conserved
1. A4 beta-galactosidase middle domain [82352]
  1. Thermus thermophilus [TaxId: 274] [82353] (2)
    1. 1kwg
      complexed with act, cl, mpd, zn
      1. region a:394-590 [77563]
    2. 1kwk
      complexed with act, cl, gal, mpd, zn
      1. region a:394-590 [77567]
DJ-1/PfpI [52325] (9)
contains a catalytic triad or dyad different from the class I GAT triad
1. Intracellular protease [52326]
  1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [52327] (1)
    1. 1g2i
      complexed with so4
      1. chain a [31438]
      2. chain b [31439]
      3. chain c [31440]
2. Hypothetical protein YhbO [89601]
  1. Escherichia coli [TaxId: 562] [89602] (1)
    1. 1oi4
      structural genomics
      1. region a:23-192 [144364]
      2. region b:223-392 [144365]
3. DJ-1 [89603]
  RNA-binding protein regulatory subunit
  1. Human (Homo sapiens) [TaxId: 9606] [89604] (20)
    SQ Q99497
    1. 1p5f
      1. chain a [94142]
    2. 1soa
      1. chain a [105843]
    3. 2or3
      automatically matched to d1pdwg_
      complexed with so4
      1. region a:2-188 [139256]
    4. 2or3
      automatically matched to d1pdwg_
      complexed with so4
      1. region b:2-188 [139257]
    5. 2r1u
      automatically matched to d1pdwg_
      1. region a:2-188 [151527]
    6. 2r1u
      automatically matched to d1pdwg_
      1. region b:2-188 [151528]
    7. 1q2u
      1. chain a [95642]
    8. 1ps4
      1. chain a [95068]
    9. 1pe0
      mutant
      1. chain a [88045]
      2. chain b [88046]
    10. 1pdv
      complexed with mse
      1. chain a [88036]
    11. 1ucf
      1. chain a [99173]
      2. chain b [99174]
    12. 1pdw
      complexed with mse
      1. chain a [88037]
      2. chain b [88038]
      3. chain c [88039]
      4. chain d [88040]
      5. chain e [88041]
      6. chain f [88042]
      7. chain g [88043]
      8. chain h [88044]
    13. 1j42
      1. chain a [90837]
    14. 3bwe
      automatically matched to d1pdwg_
      complexed with po4
      1. region a:2-188 [155686]
    15. 3bwe
      automatically matched to d1pdwg_
      complexed with po4
      1. region b:202-388 [155687]
    16. 3bwe
      automatically matched to d1pdwg_
      complexed with po4
      1. region c:402-588 [155688]
    17. 3bwe
      automatically matched to d1pdwg_
      complexed with po4
      1. region d:603-788 [155689]
    18. 3bwe
      automatically matched to d1pdwg_
      complexed with po4
      1. region e:802-988 [155690]
    19. 3bwe
      automatically matched to d1pdwg_
      complexed with po4
      1. region f:1003-1188 [155691]
    20. 3bwe
      automatically matched to d1pdwg_
      complexed with po4
      1. region g:1203-1388 [155692]
4. Putative sigma cross-reacting protein 27A (SCRP-27A, EllB) [89606]
  involved in an early stage of isoprenoid biosynthesis; contains a Cys-Glu putative catalytic dyad
  1. Escherichia coli [TaxId: 562] [89607] (2)
    1. 1vhq
      structural genomics
      complexed with act
      1. chain a [100696]
      2. chain b [100697]
    2. 1oy1
      structural genomics; NESG target ER105
      complexed with mse
      1. chain a [87548]
      2. chain b [87549]
      3. chain c [87550]
      4. chain d [87551]
5. HSP31 (HchA; YedU) [89609]
  contains a buried Cys-His-Asp triad within one subunit
  1. Escherichia coli [TaxId: 562] [89610] (5)
    1. 1n57
      complexed with mg, mse
      1. chain a [85328]
    2. 1ons
      complexed with zn2
      1. chain a [93371]
    3. 1izz
      1. chain a [90731]
    4. 1izy
      1. chain a [90729]
      2. chain b [90730]
    5. 1pv2
      1. chain a [95142]
      2. chain b [95143]
      3. chain c [95144]
      4. chain d [95145]
      5. chain e [95146]
      6. chain f [95147]
      7. chain g [95148]
      8. chain h [95149]
6. Hypothetical protein Ydr533Cp [102253]
  contains a buried Cys-His-Glu triad within one subunit
  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102254] (4)
    1. 1qvz
      structural genomics
      mutant
      1. chain a [96453]
      2. chain b [96454]
    2. 1qvw
      structural genomics
      complexed with gol; mutant
      1. chain a [96446]
      2. chain b [96447]
    3. 1rw7
      1. chain a [97963]
    4. 1qvv
      structural genomics
      1. chain a [96442]
      2. chain b [96443]
      3. chain c [96444]
      4. chain d [96445]
7. GK2698 ortholog [117481]
  1. Bacillus stearothermophilus [TaxId: 1422] [117482] (1)
    SQ Q5KWF3; 96% sequence identity; Geobacillus kaustophilus TaxID: 1462
    1. 1u9c
      Structural genomics target; APC35852
      1. chain a [113234]
8. Protein ThiJ (YajL) [142070]
  1. Escherichia coli [TaxId: 562] [142071] (2)
    SQ Q46948 2-196
    1. 2ab0
      1. region a:2-196 [126501]
    2. 2ab0
      automatically matched to 2AB0 A:2-196
      1. region b:2-196 [126502]
9. Hypothetical protein Atu0886 [142072]
  1. Agrobacterium tumefaciens [TaxId: 358] [142073] (3)
    SQ Q8UGZ9 1-188
    1. 2fex
      complexed with gol, so4
      1. region a:1-188 [133354]
    2. 2fex
      automatically matched to 2FEX A:1-188
      complexed with gol, so4
      1. region b:1-188 [133355]
    3. 2fex
      automatically matched to 2FEX A:1-188
      complexed with gol, so4
      1. region c:1-188 [133356]
Catalase, C-terminal domain [52328] (2)
1. Catalase, C-terminal domain [52329]
  1. Escherichia coli, HPII [TaxId: 562] [52330] (14)
    1. 1p80
      complexed with hem; mutant
      1. region a:598-753 [94337]
      2. region b:598-753 [94339]
      3. region c:598-753 [94341]
      4. region d:598-753 [94343]
    2. 1p81
      complexed with hdd; mutant
      1. region a:598-753 [94345]
      2. region b:598-753 [94347]
      3. region c:598-753 [94349]
      4. region d:598-753 [94351]
    3. 1gge
      complexed with hdd
      1. region a:598-753 [31449]
      2. region b:598-753 [31450]
      3. region c:598-753 [31451]
      4. region d:598-753 [31452]
    4. 1gg9
      complexed with hem; mutant
      1. region a:598-753 [31445]
      2. region b:598-753 [31446]
      3. region c:598-753 [31447]
      4. region d:598-753 [31448]
    5. 1cf9
      complexed with hem; mutant
      1. region a:598-753 [31441]
      2. region b:598-753 [31442]
      3. region c:598-753 [31443]
      4. region d:598-753 [31444]
    6. 1qws
      complexed with hem; mutant
      1. region a:598-753 [96493]
      2. region b:598-753 [96495]
      3. region c:598-753 [96497]
      4. region d:598-753 [96499]
    7. 1ggj
      complexed with hdd; mutant
      1. region a:598-753 [31457]
      2. region b:598-753 [31458]
      3. region c:598-753 [31459]
      4. region d:598-753 [31460]
    8. 1qf7
      complexed with hem; mutant
      1. region a:598-753 [31461]
      2. region b:598-753 [31462]
      3. region c:598-753 [31463]
      4. region d:598-753 [31464]
    9. 1p7z
      complexed with hem; mutant
      1. region a:598-753 [94329]
      2. region b:598-753 [94331]
      3. region c:598-753 [94333]
      4. region d:598-753 [94335]
    10. 1ggh
      complexed with hem; mutant
      1. region a:598-753 [31465]
      2. region b:598-753 [31466]
      3. region c:598-753 [31467]
      4. region d:598-753 [31468]
    11. 1ggk
      complexed with hem; mutant
      1. region a:598-753 [31453]
      2. region b:598-753 [31454]
      3. region c:598-753 [31455]
      4. region d:598-753 [31456]
    12. 1p7y
      complexed with hem; mutant
      1. region a:598-753 [94321]
      2. region b:598-753 [94323]
      3. region c:598-753 [94325]
      4. region d:598-753 [94327]
    13. 1ggf
      complexed with hem, peo; mutant
      1. region a:598-753 [31469]
      2. region b:598-753 [31470]
      3. region c:598-753 [31471]
      4. region d:598-753 [31472]
    14. 1iph
      complexed with hem
      1. region a:598-753 [31473]
      2. region b:598-753 [31474]
      3. region c:598-753 [31475]
      4. region d:598-753 [31476]
  2. Neurospora crassa [TaxId: 5141] [117483] (1)
    SQ Q9C168 68-765
    1. 1sy7
      complexed with hdd, hem
      1. region a:553-736 [112161]
      2. region b:553-736 [112162]
Aspartyl dipeptidase PepE [52331] (1)
probable circular permutation in the common core; contains a catalytic Ser-His-Glu triad
1. Aspartyl dipeptidase PepE [52332]
  1. Salmonella typhimurium [TaxId: 90371] [52333] (2)
    1. 1fye
      complexed with cd
      1. chain a [31477]
    2. 1fy2
      complexed with cd
      1. chain a [31478]
ThuA-like [110486] (1)
Pfam 06283; overall fold is very similar the class I GAT family but the putative active site has a different structure
1. GK2113 homologue [110487]
  1. Bacillus stearothermophilus [TaxId: 1422] [110488] (1)
    SQ Q5KY38 # 99% sequence identity (Geobacillus kaustophilus TaxID:1462)
    1. 1t0b
      Structural genomics target
      complexed with zn
      1. chain a [106199]
      2. chain b [106200]
      3. chain c [106201]
      4. chain d [106202]
      5. chain e [106203]
      6. chain f [106204]
      7. chain g [106205]
      8. chain h [106206]
LD-carboxypeptidase A N-terminal domain-like [142074] (1)
N-terminal half of Pfam 02016
1. LD-carboxypeptidase A, N-terminal domain [142075]
  1. Pseudomonas aeruginosa [TaxId: 287] [142076] (8)
    SQ Q9HTZ1 3-169! SQ Q9HTZ1 5-142! SQ Q9HTZ1 5-169
    1. 1zl0
      complexed with edo, gol, k, na, peg, tla
      1. region a:3-169 [125232]
    2. 1zl0
      automatically matched to 1ZL0 A:3-169
      complexed with edo, gol, k, na, peg, tla
      1. region b:7-169 [125234]
    3. 1zrs
      1. region a:5-169 [125557]
    4. 1zrs
      automatically matched to 1ZRS A:5-169
      1. region b:7-169 [125559]
    5. 2aun
      mutant
      1. region a:5-142 [127335]
    6. 2aun
      automatically matched to 2AUN A:5-142
      mutant
      1. region b:7-142 [127337]
    7. 2aum
      mutant
      1. region a:5-142 [127331]
    8. 2aum
      automatically matched to 2AUM A:5-142
      mutant
      1. region b:7-142 [127333]
HTS-like [142077] (1)
Pfam 04204
1. Homoserine O-succinyltransferase HTS (MetA) [142078]
  1. Bacillus cereus [TaxId: 1396] [142079] (1)
    SQ Q72X44 17-297
    1. 2ghr
      complexed with so4
      1. region a:17-297 [135208]
STM3548-like [159492] (1)
Pfam 07090; DUF1355
1. Putative cytoplasmic protein STM3548 [159493]
  1. Salmonella typhimurium [TaxId: 90371] [159494] (6)
    SQ Q8ZLF9 8-253
    1. 2gk3
      complexed with gol
      1. region a:8-253 [147123]
    2. 2gk3
      automatically matched to 2GK3 A:8-253
      complexed with gol
      1. region b:8-253 [147124]
    3. 2gk3
      automatically matched to 2GK3 A:8-253
      complexed with gol
      1. region c:8-253 [147125]
    4. 2gk3
      automatically matched to 2GK3 A:8-253
      complexed with gol
      1. region d:8-253 [147126]
    5. 2gk3
      automatically matched to 2GK3 A:8-253
      complexed with gol
      1. region e:8-253 [147127]
    6. 2gk3
      automatically matched to 2GK3 A:8-253
      complexed with gol
      1. region f:8-253 [147128]