Structural Classification of Proteins
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Superfamily: RmlC-like cupins

link to SUPERFAMILY database - Superfamily

Lineage:

  1. Root: scop
  2. Class: All beta proteins [48724]
  3. Fold: Double-stranded beta-helix [51181]
    one turn of helix is made by two pairs of antiparallel strands linked with short turns
    has appearance of a sandwich of distinct architecture and jelly-roll topology
  4. Superfamily: RmlC-like cupins [51182]
    link to SUPERFAMILY database - Superfamily

Families:

  1. dTDP-sugar isomerase [51183] (9)
    1. dTDP-4-dehydrorhamnose 3,5-epimerase RmlC [51184]
      synonym: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase
      1. Salmonella typhimurium [TaxId: 90371] [51185] (2) picpic
      2. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [51186] (2) picpic
      3. Streptococcus suis [TaxId: 1307] [89402] (7) picpic
      4. Mycobacterium tuberculosis [TaxId: 1773] [101971] (6) picpic
      5. Pseudomonas aeruginosa [TaxId: 287] [101972] (4) picpic
      6. Archaeon Sulfolobus tokodaii [TaxId: 111955] [141586] (2) picpic
        SQ Q96Z62 1-176
    2. dTDP-4-keto-6-deoxy-glucose-5-epimerase EvaD [101973]
      1. Amycolatopsis orientalis [TaxId: 31958] [101974] (2) picpic
        SQ O52806
    3. Novobiocin biosynthesis protein NovW [141587]
      1. Streptomyces caeruleus [TaxId: 195949] [141588] (1) picpic
        SQ Q9L9E5 1-190
    4. dTDP-6-deoxy-3,4-keto-hexulose isomerase FdtA [159287]
      1. Aneurinibacillus thermoaerophilus [TaxId: 143495] [159288] (8) picpic
        SQ Q6T1W8 1-136! SQ Q6T1W8 2-136
  2. Glucose-6-phosphate isomerase, GPI [89403] (2)
    1. Glucose-6-phosphate isomerase, GPI [89404]
      Type II phosphoglucose isomerase
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [89405] (6) picpic
        SQ P83194
      2. Archaeon Thermococcus litoralis [TaxId: 2265] [101975] (11) picpic
  3. Hypothetical protein TM1112 [89406] (1)
    1. Hypothetical protein TM1112 [89407]
      1. Thermotoga maritima [TaxId: 2336] [89408] (2) picpic
  4. TM1287-like [89409] (4)
    1. Hypothetical protein TM1287 [89410]
      1. Thermotoga maritima [TaxId: 2336] [89411] (1) picpic
    2. Hypothetical protein TTHA0104 [117310]
      1. Thermus thermophilus [TaxId: 274] [117311] (3) picpic
        SQ Q5SM39
    3. Hypothetical protein TM1010 [141589]
      1. Thermotoga maritima [TaxId: 2336] [141590] (4) picpic
        SQ Q9X0A3 2-135
    4. Hypothetical protein SPy1581 [141591]
      1. Streptococcus pyogenes [TaxId: 1314] [141592] (1) picpic
        SQ Q99YR1 1-112
  5. TM1459-like [101976] (2)
    1. Hypothetical protein TM1459 [101977]
      1. Thermotoga maritima [TaxId: 2336] [101978] (1) picpic
    2. Hydroxypropylphosphonic acid epoxidase Fom4, C-terminal domain [141593]
      1. Streptomyces wedmorensis [TaxId: 43759] [141594] (20) picpic
        SQ Q56185 77-198
  6. Germin/Seed storage 7S protein [51187] (9)
    1. Germin [63853]
      Metal (manganese)-binding protein with oxalate oxidase and superoxide dismutase activities; homohexamer
      1. Barley (Hordeum vulgare) [TaxId: 4513] [63854] (5) picpic
    2. Auxin binding protein [75030]
      1. Maize (Zea mays) [TaxId: 4577] [75031] (2) picpic
    3. Seed storage 7S protein [51188]
      duplication: consists of two germin-like domains spatially arranged as subunits in the RmlC dimer; trimer is similar to the germin hexamer
      1. French bean (Phaseolus vulgaris), phaseolin [TaxId: 3885] [51189] (2) picpic
      2. Jack bean (Canavalia ensiformis), canavalin/vinculin [TaxId: 3823] [51190] (8) picpic
      3. Soybean (Glycine max), proglycinin [TaxId: 3847] [69345] (3) picpic
      4. Soybean (Glycine max), beta-conglycinin beta subunit [TaxId: 3847] [109608] (3) picpic
        SQ P25974
      5. Soybean (Glycine max), glycinin A3B4 [TaxId: 3847] [89412] (1) picpic
      6. Soybean (Glycine max), beta-conglycinin alpha prime subunit [TaxId: 3847] [110313] (1) picpic
        SQ Q7XXT2 204-621
    4. Oxalate decarboxylase OxdC (YvrK) [75033]
      duplication: consists of two germin-like metal-ion binding domains
      1. Bacillus subtilis [TaxId: 1423] [75034] (3) picpic
  7. YlbA-like [101979] (4)
    Pfam 05899; formerly pfam06038; duplication: consists of two germin-like domains
    1. Hypothetical protein YlbA [101980]
      1. Escherichia coli [TaxId: 562] [101981] (1) picpic
    2. Glyoxylate-induced protein PA1140 [101982]
      1. Pseudomonas aeruginosa [TaxId: 287] [101983] (1) picpic
    3. Hypothetical protein EF2996 [110314]
      1. Enterococcus faecalis [TaxId: 1351] [110315] (1) picpic
        SQ Q82ZQ3
    4. Hypothetical protein DR1152 [110316]
      1. Deinococcus radiodurans [TaxId: 1299] [110317] (1) picpic
        SQ Q9RV77
  8. Pirin-like [101984] (2)
    Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
    1. Pirin [101985]
      Bcl-3 and nuclear factor I-interacting protein
      1. Human (Homo sapiens) [TaxId: 9606] [101986] (1) picpic
    2. Hypothetical protein YhhW [141595]
      1. Escherichia coli [TaxId: 562] [141596] (1) picpic
        SQ P46852 1-231
  9. Quercetin 2,3-dioxygenase-like [75035] (2)
    Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
    1. Quercetin 2,3-dioxygenase [75036]
      1. Aspergillus japonicus [TaxId: 34381] [75037] (5) picpic
    2. Hypothetical protein YxaG [141597]
      1. Bacillus subtilis [TaxId: 1423] [141598] (2) picpic
        SQ P42106 5-334
  10. Type I phosphomannose isomerase [51191] (3)
    Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
    1. Phosphomannose isomerase [51192]
      1. Yeast (Candida albicans) [TaxId: 5476] [51193] (1) picpic
        contains insert all-alpha subdomain; residues 152-266
    2. Mannose-6-phosphate isomerase ManA [101987]
      1. Bacillus subtilis [TaxId: 1423] [101988] (1) picpic
    3. Putative mannosephosphate isomerase AF0035 [141599]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [141600] (1) picpic
        SQ O30200 1-299
  11. Homogentisate dioxygenase [51194] (1)
    Share a common two-domain fold with the 7S protein; there is a metal-binding site in the C-terminal domain similar to the metal-binding site of germin
    1. Homogentisate dioxygenase [51195]
      1. Human (Homo sapiens) [TaxId: 9606] [51196] (2) picpic
  12. Acireductone dioxygenase [82191] (2)
    1. Acireductone dioxygenase [82192]
      1. Klebsiella pneumoniae [TaxId: 573] [82193] (1) picpic
        NMR-derived model
      2. Mouse (Mus musculus) [TaxId: 10090] [141601] (1) picpic
        SQ Q99JT9 1-179
  13. KduI-like [110318] (2)
    Pfam 04962: duplication: consists of two germin-like domains
    1. 5-keto-4-deoxyuronate isomerase KduI [110319]
      1. Escherichia coli [TaxId: 562] [110320] (3) picpic
        SQ Q46938 1-266
      2. Enterococcus faecalis [TaxId: 1351] [141602] (6) picpic
        SQ Q838L9 1-260
  14. Ureidoglycolate hydrolase AllA [117312] (3)
    Pfam 04115; beta-hairpin-swapped dimeric protein of the germin-like fold
    1. Ureidoglycolate hydrolase AllA [117313]
      1. Shigella flexneri [TaxId: 623] [117314] (2) picpic
        SQ P77731 ! SQ P63487
      2. Pseudomonas putida [TaxId: 303] [141603] (2) picpic
        SQ P59285 1-166
      3. Escherichia coli [TaxId: 562] [141604] (2) picpic
        SQ P63486 1-160
  15. Probable transcriptional regulator VC1968, C-terminal domain [117315] (1)
    1. Probable transcriptional regulator VC1968, C-terminal domain [117316]
      1. Vibrio cholerae [TaxId: 666] [117317] (1) picpic
        SQ Q9KQN0
  16. YML079-like [117318] (3)
    Pfam 06172; DUF985
    1. Hypothetical protein YML079W [117319]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117320] (2) picpic
        SQ Q03629
    2. Hypothetical protein Atu3615 [141605]
      1. Agrobacterium tumefaciens [TaxId: 358] [141606] (7) picpic
        SQ Q8U9W0 4-143
    3. Hypothetical protein SO0799 [141607]
      1. Shewanella oneidensis [TaxId: 70863] [141608] (10) picpic
        SQ Q8EIN8 1-158
  17. PA5104-like [141609] (1)
    Pfam 05962; DUF886; duplication: consists of two germin-like domains; overall structural similarity to the YlbA-like family (scop_fa 101979) except a deletion in the interdomain linker region
    1. Hypothetical protein PA5104 [141610]
      1. Pseudomonas aeruginosa [TaxId: 287] [141611] (4) picpic
        SQ Q9HU79 2-196
  18. MJ0764-like [141612] (1)
    1. Hypothetical protein MJ0764 [141613]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [141614] (1) picpic
        SQ Q58174 1-108
  19. Cysteine dioxygenase type I [141615] (4)
    Pfam 05995, CDO_I
    1. Cysteine dioxygenase type I [141616]
      1. Mouse (Mus musculus) [TaxId: 10090] [141617] (4) picpic
        SQ P60334 5-190
      2. Ralstonia eutropha [TaxId: 106590] [159289] (1) picpic
        SQ Q46R41 11-202
      3. Human (Homo sapiens) [TaxId: 9606] [159290] (1) picpic
        SQ Q16878 6-190
      4. Rattus norvegicus [TaxId: 10116] [159291] (1) picpic
  20. 3-hydroxyanthranilic acid dioxygenase-like [141618] (2)
    Pfam 06052; 3-HAO
    1. 3-hydroxyanthranilate-3,4-dioxygenase [141619]
      1. Ralstonia metallidurans [TaxId: 119219] [141620] (4) picpic
        SQ Q1LCS4 1-174
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [159292] (2) picpic
        SQ P47096 1-175
  21. Acetylacetone-cleaving enzyme-like [159293] (1)
    PfamB 026844
    1. Putative acetyl/propionyl-CoA carboxylase subunit alpha Mpe_A3659 [159294]
      1. Rubrivivax gelatinosus [TaxId: 28068] [159295] (2) picpic
        SQ A2SM23 1-144
  22. VPA0057-like [159296] (1)
    Pfam 06865; DUF1255; non-canonical dimerisation mode
    1. Uncharacterized protein VPA0057 [159297]
      1. Vibrio parahaemolyticus [TaxId: 670] [159298] (1) picpic
        SQ Q87K41 2-94
  23. Gentisate 1,2-dioxygenase-like [159299] (3)
    Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin; homotetramer
    1. Gentisate 1,2-dioxygenase [159300]
      Salicylate 1,2-dioxygenase
      1. Escherichia coli [TaxId: 562] [159301] (4) picpic
        SQ Q8X655 35-342
      2. Silicibacter pomeroyi [TaxId: 89184] [159302] (2) picpic
        SQ Q5LLB1 19-373
      3. Pseudaminobacter salicylatoxidans [TaxId: 93369] [159303] (4) picpic
        SQ Q67FT0 17-367
  24. EutQ-like [159304] (1)
    Pfam 06249
    1. Ethanolamine utilization protein EutQ [159305]
      1. Salmonella typhimurium [TaxId: 90371] [159306] (2) picpic
        SQ Q9ZFV5 100-227
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MRC site Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009
Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk