SCOPe 2.02: Protein: D-xylose isomerase

Lineage for Protein: D-xylose isomerase

Root: SCOPe 2.02
Class c: Alpha and beta proteins (a/b) [51349] (147 folds)

Fold c.1: TIM beta/alpha-barrel [51350] (33 superfamilies)
contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
the first seven superfamilies have similar phosphate-binding sites

Superfamily c.1.15: Xylose isomerase-like [51658] (8 families)
different families share similar but non-identical metal-binding sites
Family c.1.15.3: Xylose isomerase [51665] (2 proteins)
Protein D-xylose isomerase [51666] (13 species)

Species:

Actinoplanes missouriensis [TaxId:1866] [51673] (14 PDB entries)
1. Domains for 1bhw:
  1. Domain d1bhwa_: 1bhw A: [29525]
  2. Domain d1bhwb_: 1bhw B: [29526]
  3. Domain d1bhwc_: 1bhw C: [29527]
  4. Domain d1bhwd_: 1bhw D: [29528]
2. Domains for 1xim:
  1. Domain d1xima_: 1xim A: [29473]
    complexed with co, xyl
  2. Domain d1ximb_: 1xim B: [29474]
    complexed with co, xyl
  3. Domain d1ximc_: 1xim C: [29475]
    complexed with co, xyl
  4. Domain d1ximd_: 1xim D: [29476]
    complexed with co, xyl
3. Domains for 1xin:
  1. Domain d1xina_: 1xin A: [29513]
    complexed with mg, xyl
  2. Domain d1xinb_: 1xin B: [29514]
    complexed with mg, xyl
  3. Domain d1xinc_: 1xin C: [29515]
    complexed with mg, xyl
  4. Domain d1xind_: 1xin D: [29516]
    complexed with mg, xyl
4. Domains for 2xim:
  1. Domain d2xima_: 2xim A: [29497]
    complexed with mg, xyl
  2. Domain d2ximb_: 2xim B: [29498]
    complexed with mg, xyl
  3. Domain d2ximc_: 2xim C: [29499]
    complexed with mg, xyl
  4. Domain d2ximd_: 2xim D: [29500]
    complexed with mg, xyl
5. Domains for 2xin:
  1. Domain d2xina_: 2xin A: [29493]
    complexed with co, sor
  2. Domain d2xinb_: 2xin B: [29494]
    complexed with co, sor
  3. Domain d2xinc_: 2xin C: [29495]
    complexed with co, sor
  4. Domain d2xind_: 2xin D: [29496]
    complexed with co, sor
6. Domains for 3xim:
  1. Domain d3xima_: 3xim A: [29477]
    complexed with co, sor
  2. Domain d3ximb_: 3xim B: [29478]
    complexed with co, sor
  3. Domain d3ximc_: 3xim C: [29479]
    complexed with co, sor
  4. Domain d3ximd_: 3xim D: [29480]
    complexed with co, sor
7. Domains for 3xin:
  1. Domain d3xina_: 3xin A: [29489]
  2. Domain d3xinb_: 3xin B: [29490]
  3. Domain d3xinc_: 3xin C: [29491]
  4. Domain d3xind_: 3xin D: [29492]
8. Domains for 4xim:
  1. Domain d4xima_: 4xim A: [29485]
    complexed with co
  2. Domain d4ximb_: 4xim B: [29486]
    complexed with co
  3. Domain d4ximc_: 4xim C: [29487]
    complexed with co
  4. Domain d4ximd_: 4xim D: [29488]
    complexed with co
9. Domains for 5xim:
  1. Domain d5xima_: 5xim A: [29521]
    complexed with mg, sor
  2. Domain d5ximb_: 5xim B: [29522]
    complexed with mg, sor
  3. Domain d5ximc_: 5xim C: [29523]
    complexed with mg, sor
  4. Domain d5ximd_: 5xim D: [29524]
    complexed with mg, sor
10. Domains for 5xin:
  1. Domain d5xina_: 5xin A: [29481]
    complexed with mg, xls
  2. Domain d5xinb_: 5xin B: [29482]
    complexed with mg, xls
  3. Domain d5xinc_: 5xin C: [29483]
    complexed with mg, xls
  4. Domain d5xind_: 5xin D: [29484]
    complexed with mg, xls
11. Domains for 6xim:
  1. Domain d6xima_: 6xim A: [29517]
    complexed with mg, xls
  2. Domain d6ximb_: 6xim B: [29518]
    complexed with mg, xls
  3. Domain d6ximc_: 6xim C: [29519]
    complexed with mg, xls
  4. Domain d6ximd_: 6xim D: [29520]
    complexed with mg, xls
12. Domains for 7xim:
  1. Domain d7xima_: 7xim A: [29501]
  2. Domain d7ximb_: 7xim B: [29502]
  3. Domain d7ximc_: 7xim C: [29503]
  4. Domain d7ximd_: 7xim D: [29504]
13. Domains for 8xim:
  1. Domain d8xima_: 8xim A: [29509]
    complexed with mg, xls
  2. Domain d8ximb_: 8xim B: [29510]
    complexed with mg, xls
  3. Domain d8ximc_: 8xim C: [29511]
    complexed with mg, xls
  4. Domain d8ximd_: 8xim D: [29512]
    complexed with mg, xls
14. Domains for 9xim:
  1. Domain d9xima_: 9xim A: [29505]
    complexed with mn, xls
  2. Domain d9ximb_: 9xim B: [29506]
    complexed with mn, xls
  3. Domain d9ximc_: 9xim C: [29507]
    complexed with mn, xls
  4. Domain d9ximd_: 9xim D: [29508]
    complexed with mn, xls
Arthrobacter, strain b3728 [TaxId:1663] [51672] (17 PDB entries)
1. Domains for 1did:
  1. Domain d1dida_: 1did A: [29459]
    complexed with dig, mn
  2. Domain d1didb_: 1did B: [29460]
    complexed with dig, mn
2. Domains for 1die:
  1. Domain d1diea_: 1die A: [29443]
    complexed with mg, noj
  2. Domain d1dieb_: 1die B: [29444]
    complexed with mg, noj
3. Domains for 1xla:
  1. Domain d1xlaa_: 1xla A: [29445]
  2. Domain d1xlab_: 1xla B: [29446]
4. Domains for 1xlb:
  1. Domain d1xlba_: 1xlb A: [29465]
    complexed with mg
  2. Domain d1xlbb_: 1xlb B: [29466]
    complexed with mg
5. Domains for 1xlc:
  1. Domain d1xlca_: 1xlc A: [29447]
    complexed with mg, xyl
  2. Domain d1xlcb_: 1xlc B: [29448]
    complexed with mg, xyl
6. Domains for 1xld:
  1. Domain d1xlda_: 1xld A: [29449]
    complexed with mn, xyl
  2. Domain d1xldb_: 1xld B: [29450]
    complexed with mn, xyl
7. Domains for 1xle:
  1. Domain d1xlea_: 1xle A: [29471]
    complexed with mn
  2. Domain d1xleb_: 1xle B: [29472]
    complexed with mn
8. Domains for 1xlf:
  1. Domain d1xlfa_: 1xlf A: [29451]
    complexed with gco, mn
  2. Domain d1xlfb_: 1xlf B: [29452]
    complexed with gco, mn
9. Domains for 1xlg:
  1. Domain d1xlga_: 1xlg A: [29461]
    complexed with al, mg, xyl
  2. Domain d1xlgb_: 1xlg B: [29462]
    complexed with al, mg, xyl
10. Domains for 1xlh:
  1. Domain d1xlha_: 1xlh A: [29453]
    complexed with al
  2. Domain d1xlhb_: 1xlh B: [29454]
    complexed with al
11. Domains for 1xli:
  1. Domain d1xlia_: 1xli A: [29455]
    complexed with glt, mn
  2. Domain d1xlib_: 1xli B: [29456]
    complexed with glt, mn
12. Domains for 1xlj:
  1. Domain d1xlja_: 1xlj A: [29463]
    complexed with mn, xyl
  2. Domain d1xljb_: 1xlj B: [29464]
    complexed with mn, xyl
13. Domains for 1xlk:
  1. Domain d1xlka_: 1xlk A: [29469]
    complexed with mn
  2. Domain d1xlkb_: 1xlk B: [29470]
    complexed with mn
14. Domains for 1xll:
  1. Domain d1xlla_: 1xll A: [29467]
    complexed with zn
  2. Domain d1xllb_: 1xll B: [29468]
    complexed with zn
15. Domains for 1xlm:
  1. Domain d1xlma_: 1xlm A: [29441]
    complexed with al, xyl; mutant
  2. Domain d1xlmb_: 1xlm B: [29442]
    complexed with al, xyl; mutant
16. Domains for 4xia:
  1. Domain d4xiaa_: 4xia A: [29439]
    complexed with mg, sor
  2. Domain d4xiab_: 4xia B: [29440]
    complexed with mg, sor
17. Domains for 5xia:
  1. Domain d5xiaa_: 5xia A: [29457]
    complexed with mg, xyl
  2. Domain d5xiab_: 5xia B: [29458]
    complexed with mg, xyl
Bacillus stearothermophilus [TaxId:1422] [51675] (1 PDB entry)
- Domains for 1a0d:
  1. Domain d1a0da_: 1a0d A: [29533]
    complexed with mn
  2. Domain d1a0db_: 1a0d B: [29534]
    complexed with mn
  3. Domain d1a0dc_: 1a0d C: [29535]
    complexed with mn
  4. Domain d1a0dd_: 1a0d D: [29536]
    complexed with mn
Clostridium thermosulfurogenes, also known as Thermoanaerobacter thermosulfurigenes [TaxId:33950] [51674] (1 PDB entry)
- Domains for 1a0c:
  1. Domain d1a0ca_: 1a0c A: [29529]
    complexed with co
  2. Domain d1a0cb_: 1a0c B: [29530]
    complexed with co
  3. Domain d1a0cc_: 1a0c C: [29531]
    complexed with co
  4. Domain d1a0cd_: 1a0c D: [29532]
    complexed with co
Streptomyces albus [TaxId:1888] [51667] (1 PDB entry)
- Domain for 6xia:
  - Domain d6xiaa_: 6xia A: [29406]
Streptomyces diastaticus, M1033 [TaxId:1956] [51671] (2 PDB entries)
1. Domain for 1clk:
  - Domain d1clka_: 1clk A: [29438]
    complexed with co, mg
2. Domains for 1qt1:
  1. Domain d1qt1a_: 1qt1 A: [29436]
    complexed with co
  2. Domain d1qt1b_: 1qt1 B: [29437]
    complexed with co
Streptomyces murinus [TaxId:33900] [51668] (1 PDB entry)
- Domains for 1dxi:
  1. Domain d1dxia_: 1dxi A: [29407]
    complexed with mg
  2. Domain d1dxib_: 1dxi B: [29408]
    complexed with mg
Streptomyces olivochromogenes [TaxId:1963] [51669] (9 PDB entries)
1. Domain for 1muw:
  - Domain d1muwa_: 1muw A: [79495]
    atomic resolution structure
    complexed with mg, mn, oh
2. Domain for 1s5m:
  - Domain d1s5ma_: 1s5m A: [98565]
    complexed with glc, mn, na
3. Domain for 1s5n:
  - Domain d1s5na_: 1s5n A: [98566]
    complexed with mn, na, oh, xyl
4. Domains for 1xya:
  1. Domain d1xyaa_: 1xya A: [29411]
    complexed with mg, oh
  2. Domain d1xyab_: 1xya B: [29412]
    complexed with mg, oh
5. Domains for 1xyb:
  1. Domain d1xyba_: 1xyb A: [29417]
    complexed with glo, mg
  2. Domain d1xybb_: 1xyb B: [29418]
    complexed with glo, mg
6. Domains for 1xyc:
  1. Domain d1xyca_: 1xyc A: [29419]
    complexed with 3mf, mg
  2. Domain d1xycb_: 1xyc B: [29420]
    complexed with 3mf, mg
7. Domains for 1xyl:
  1. Domain d1xyla_: 1xyl A: [29413]
    complexed with mg, oh
  2. Domain d1xylb_: 1xyl B: [29414]
    complexed with mg, oh
8. Domains for 1xym:
  1. Domain d1xyma_: 1xym A: [29415]
    complexed with glo, mg, oh
  2. Domain d1xymb_: 1xym B: [29416]
    complexed with glo, mg, oh
9. Domains for 2gyi:
  1. Domain d2gyia_: 2gyi A: [29409]
    complexed with hya, mg
  2. Domain d2gyib_: 2gyi B: [29410]
    complexed with hya, mg
Streptomyces rubiginosus [TaxId:1929] [51670] (28 PDB entries)
1. Domain for 1gw9:
  - Domain d1gw9a_: 1gw9 A: [70658]
    complexed with ca, iod, lxc
2. Domain for 1mnz:
  - Domain d1mnza_: 1mnz A: [79328]
    atomic resolution structure
    complexed with ca, mg, mrd, trs
3. Domains for 1o1h:
  1. Domain d1o1ha_: 1o1h A: [81044]
    complexed with ca, cl, kr, mg, mpd, trs
  2. Domain d1o1hb_: 1o1h B: [81045]
    complexed with ca, cl, kr, mg, mpd, trs
4. Domains for 1oad:
  1. Domain d1oada_: 1oad A: [81253]
    complexed with mg, mn, mpd, mqd, mrd, trs
  2. Domain d1oadb_: 1oad B: [81254]
    complexed with mg, mn, mpd, mqd, mrd, trs
5. Domain for 1xib:
  - Domain d1xiba_: 1xib A: [29424]
    complexed with mn
6. Domain for 1xic:
  - Domain d1xica_: 1xic A: [29425]
    complexed with mn, xls
7. Domain for 1xid:
  - Domain d1xida_: 1xid A: [29431]
    complexed with asc, mn
8. Domain for 1xie:
  - Domain d1xiea_: 1xie A: [29433]
    complexed with aso, mn
9. Domain for 1xif:
  - Domain d1xifa_: 1xif A: [29426]
    complexed with glc, mn
10. Domain for 1xig:
  - Domain d1xiga_: 1xig A: [29432]
    complexed with mn, xyl
11. Domain for 1xih:
  - Domain d1xiha_: 1xih A: [29430]
    complexed with mn, sor
12. Domain for 1xii:
  - Domain d1xiia_: 1xii A: [29428]
    complexed with mn, xul
13. Domain for 1xij:
  - Domain d1xija_: 1xij A: [29429]
    complexed with mn, the
14. Domain for 1xis:
  - Domain d1xisa_: 1xis A: [29422]
    complexed with mn
15. Domain for 2xis:
  - Domain d2xisa_: 2xis A: [29427]
    complexed with mg, xyl
16. Domain for 3kbj:
  - Domain d3kbja_: 3kbj A: [179237]
    automated match to d1dxia_
17. Domain for 3kbm:
  - Domain d3kbma_: 3kbm A: [179238]
    automated match to d1dxia_
    complexed with cd, glc
18. Domain for 3kbn:
  - Domain d3kbna_: 3kbn A: [179239]
    automated match to d1dxia_
    complexed with glo, ni
19. Domain for 3kbs:
  - Domain d3kbsa_: 3kbs A: [179240]
    automated match to d1dxia_
    complexed with cd
20. Domain for 3kbv:
  - Domain d3kbva_: 3kbv A: [179241]
    automated match to d1dxia_
    complexed with ni
21. Domain for 3kbw:
  - Domain d3kbwa_: 3kbw A: [179242]
    automated match to d1dxia_
    complexed with mg, ni
22. Domain for 3kcj:
  - Domain d3kcja_: 3kcj A: [179271]
    automated match to d1dxia_
    complexed with dod
23. Domain for 3kcl:
  - Domain d3kcla_: 3kcl A: [179272]
    automated match to d1dxia_
    complexed with cd, dod, glc
24. Domain for 3kco:
  - Domain d3kcoa_: 3kco A: [179273]
    automated match to d1dxia_
    complexed with dod, glo, ni
25. Domain for 3xis:
  - Domain d3xisa_: 3xis A: [29423]
    complexed with mg, xys
26. Domain for 4xis:
  - Domain d4xisa_: 4xis A: [29421]
    complexed with mn
27. Domain for 8xia:
  - Domain d8xiaa_: 8xia A: [29435]
    complexed with mn, xls
28. Domain for 9xia:
  - Domain d9xiaa_: 9xia A: [29434]
    complexed with dfr, mn
Streptomyces sp. [TaxId:253732] [196714] (2 PDB entries)
1. Domain for 4hhl:
  - Domain d4hhla_: 4hhl A: [196715]
    automated match to d1dxia_
    complexed with co, edo, mg
2. Domain for 4hhm:
  - Domain d4hhmg_: 4hhm G: [196716]
    automated match to d1dxia_
    complexed with co, mg; mutant
Thermotoga neapolitana [TaxId:2337] [51676] (1 PDB entry)
- Domains for 1a0e:
  1. Domain d1a0ea_: 1a0e A: [29537]
    complexed with co
  2. Domain d1a0ed_: 1a0e D: [29538]
    complexed with co
Thermus aquaticus, subsp. Caldophilus [TaxId:271] [51677] (1 PDB entry)
- Domains for 1bxc:
  1. Domain d1bxca_: 1bxc A: [29539]
  2. Domain d1bxcb_: 1bxc B: [29540]
  3. Domain d1bxcc_: 1bxc C: [29541]
  4. Domain d1bxcd_: 1bxc D: [29542]
Thermus aquaticus, subsp. Thermophilus [TaxId:271] [51678] (1 PDB entry)
- Domains for 1bxb:
  1. Domain d1bxba_: 1bxb A: [29543]
  2. Domain d1bxbb_: 1bxb B: [29544]
  3. Domain d1bxbc_: 1bxb C: [29545]
  4. Domain d1bxbd_: 1bxb D: [29546]

More info for Protein D-xylose isomerase from c.1.15.3: Xylose isomerase

Timeline for Protein D-xylose isomerase from c.1.15.3: Xylose isomerase:

Protein D-xylose isomerase from c.1.15.3: Xylose isomerase first appeared (with stable ids) in SCOP 1.55
Protein D-xylose isomerase from c.1.15.3: Xylose isomerase appears in SCOPe 2.01
Protein D-xylose isomerase from c.1.15.3: Xylose isomerase appears in SCOPe 2.03
Protein D-xylose isomerase from c.1.15.3: Xylose isomerase appears in the current release, SCOPe 2.08