Structural Classification of Proteins

Fold: Rubredoxin-like

: metal(zinc or iron)-bound fold; sequence contains two CX(n)C motifs, in most cases n = 2

Lineage:

Root: scop
Class: Small proteins [56992]
Usually dominated by metal ligand, heme, and/or disulfide bridges
Fold: Rubredoxin-like [57769]
metal(zinc or iron)-bound fold; sequence contains two CX(n)C motifs, in most cases n = 2

Superfamilies:

Methionyl-tRNA synthetase (MetRS), Zn-domain [57770] (1)
uperfamily
1. Methionyl-tRNA synthetase (MetRS), Zn-domain [57771] (2)
  in the Pyrococcus abyssi MetRS structure there is a tandem repeat of two such domains swapped with their zinc-binding 'knuckles', this duplicated finger occupies a larger region (124-183) than defined below; there is a structurally equivalent region in the E. coli enzyme lacking the second zinc-binding site
  1. Methionyl-tRNA synthetase (MetRS), Zn-domain [57772]
    1. Escherichia coli [TaxId: 562] [57773] (9)
    2. Pyrococcus abyssi [TaxId: 29292] [111451] (1)
      SQ Q9V011 1-606; C-domain 616-722 is solved separately: 1MKH
Microbial and mitochondrial ADK, insert "zinc finger" domain [57774] (1)
uperfamily
1. Microbial and mitochondrial ADK, insert "zinc finger" domain [57775] (8)
  1. Microbial and mitochondrial ADK, insert "zinc finger" domain [57776]
    1. Bacillus stearothermophilus [TaxId: 1422] [57777] (3)
    2. Bacillus subtilis [TaxId: 1423] [103618] (1)
    3. Bacillus globisporus [TaxId: 1459] [103619] (1)
    4. Escherichia coli [TaxId: 562] [57778] (6)
      contains a rudiment form of the domain that lacks zn-binding site
    5. Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913] [57779] (1)
      contains a rudiment "zinc-finger" subdomain
    6. Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913] [57780] (2)
      contains a rudiment "zinc-finger" subdomain
    7. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57781] (4)
      contains a rudiment "zinc-finger" subdomain
    8. Maize (Zea mays) [TaxId: 4577] [57782] (1)
NADH pyrophosphatase intervening domain [116738] (1)
uperfamily
1. NADH pyrophosphatase intervening domain [116739] (1)
  1. NADH pyrophosphatase intervening domain [116740]
    1. Escherichia coli [TaxId: 562] [116741] (1)
Zinc beta-ribbon [57783] (5)
uperfamily
1. Transcriptional factor domain [57784] (6)
  1. Transcriptional factor SII, C-terminal domain [57785]
    1. Human (Homo sapiens) [TaxId: 9606] [57786] (1)
  2. Transcription initiation factor TFIIB, N-terminal domain [57789]
    1. Archaeon Pyrococcus furiosus [TaxId: 2261] [57790] (1)
    2. Human (Homo sapiens) [TaxId: 9606] [57791] (3)
      SQ Q00403 2-59
  3. RBP9 subunit of RNA polymerase II [57787]
    contains two differently decorated domains of this fold
    1. Archaeon Thermococcus celer [TaxId: 2264] [57788] (1)
    2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64575] (41)
      SQ P27999; part of multichain biological unit
  4. Transcription initiation factor TFIIE-alpha [118283]
    1. Human (Homo sapiens) [TaxId: 9606] [118284] (1)
      SQ P29083 113-174
2. DNA primase zinc finger [57792] (2)
  contains alpha-helices in the N- and C-terminal extensions (linkers?)
  1. Zinc-binding domain of DNA primase [57793]
    1. Bacillus stearothermophilus [TaxId: 1422] [57794] (1)
  2. Zinc-binding domain of primase-helicase [90207]
    1. Bacteriophage T7 [TaxId: 10760] [90208] (1)
3. Prokaryotic DNA topoisomerase I, a C-terminal fragment [57795] (1)
  Duplication: contains tandem repeats of several domains with zinc-binding sites being lost in some of them
  1. Prokaryotic DNA topoisomerase I, a C-terminal fragment [57796]
    1. Escherichia coli [TaxId: 562] [57797] (1)
4. Putative zinc binding domain [118285] (1)
  Pfam 05129; DUF701
  1. Hypothetical UPF0222 protein MGC4549 [118286]
    1. Mouse (Mus musculus) [TaxId: 10090] [118287] (1)
      SQ P60003
5. PhnA zinc-binding domain [144191] (1)
  Pfam 08274
  1. Hypothetical protein PA0128, N-terminal domain [144192]
    1. Pseudomonas aeruginosa [TaxId: 287] [144193] (1)
      SQ Q9I704 2-39
Casein kinase II beta subunit [57798] (1)
uperfamily
1. Casein kinase II beta subunit [57799] (3)
  contains alpha-helices in the N- and C-terminal extensions (linkers?)
  1. Casein kinase II beta subunit [57800]
    1. Human (Homo sapiens) [TaxId: 9606] [57801] (4)
    2. African clawed frog (Xenopus laevis) [TaxId: 8355] [118288] (1)
      SQ P28021 7-178 # 100% identical to the human enzyme (SQ P13862 7-178)
    3. Rattus norvegicus [TaxId: 10116] [161172] (2)
Rubredoxin-like [57802] (3)
uperfamily
1. Rubredoxin [57803] (10)
  1. Rubredoxin [57804]
    1. Desulfovibrio vulgaris [TaxId: 881] [57805] (7)
    2. Desulfovibrio gigas [TaxId: 879] [57806] (3)
    3. Desulfovibrio desulfuricans, strain 27774 [TaxId: 876] [57807] (1)
    4. Clostridium pasteurianum [TaxId: 1501] [57808] (23)
      SQ P00268
    5. Archaeon Pyrococcus furiosus [TaxId: 2261] [57809] (11)
      SQ P24297
    6. Guillardia theta [TaxId: 55529] [57810] (2)
  2. Two-iron rubredoxin [103620]
    1. Pseudomonas oleovorans [TaxId: 301] [103621] (1)
  3. Rubrerythrin, C-terminal domain [57811]
    1. Desulfovibrio vulgaris [TaxId: 881] [57812] (10)
      SQ P24931
    2. Archaeon Pyrococcus furiosus [TaxId: 2261] [103622] (3)
  4. Nigerythrin, C-terminal domain [144194]
    1. Desulfovibrio vulgaris [TaxId: 881] [144195] (6)
      SQ P30820 167-202
2. Desulforedoxin [57813] (3)
  1. Desulforedoxin [57814]
    dimeric mono-domain protein with two rubredoxin-type metal centres
    1. Desulfovibrio gigas [TaxId: 879] [57815] (4)
  2. Desulfoferrodoxin N-terminal domain [57816]
    1. Desulfovibrio desulfuricans [TaxId: 876] [57817] (13)
    2. Desulfoarculus baarsii (Desulfovibrio baarsii) [TaxId: 887] [111452] (3)
      SQ Q46495
3. Cytochrome c oxidase Subunit F [57818] (1)
  membrane-anchored rubredoxin-like domain
  1. Cytochrome c oxidase Subunit F [57819]
    1. Cow (Bos taurus) [TaxId: 9913] [57820] (21)
Zn-finger domain of Sec23/24 [82919] (1)
uperfamily
1. Zn-finger domain of Sec23/24 [82920] (2)
  1. Sec23 [82921]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82922] (3)
  2. Sec24 [82923]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82924] (4)
Ran binding protein zinc finger-like [90209] (1)
contains CxxxxC-x(n)-CxxC zinc-binding site; similar to the Sec23/24 zinc finger domain
uperfamily
1. Ran binding protein zinc finger-like [90210] (6)
  1. Znf265, first zinc-finger domain [90211]
    1. Human (Homo sapiens) [TaxId: 9606] [90212] (1)
  2. Npl4 [90215]
    a ubiquitin-interacting domain
    1. Rat (Rattus norvegicus) [TaxId: 10116] [90216] (2)
  3. MDM4 [144196]
    1. Human (Homo sapiens) [TaxId: 9606] [144197] (1)
      SQ O15151 300-340
  4. MDM2 [144198]
    1. Human (Homo sapiens) [TaxId: 9606] [144199] (2)
      SQ Q00987 290-335
  5. Vacuolar protein-sorting-associated protein 36, VPS36 [161173]
    1. Saccharomyces cerevisiae [TaxId: 4932] [161174] (2)
      SQ Q06696 115-161
  6. Nuclear pore complex protein nup153 [161175]
    1. Human (Homo sapiens) [TaxId: 9606] [161176] (1)
      SQ P49790 722-750
Hypothetical protein Ta0289 C-terminal domain [103623] (1)
contains CxxC-x(n)-CxxxxC zinc-binding site; sequence similarity to NAD-dependent DNA ligase zinc-finger subdomain
uperfamily
1. Hypothetical protein Ta0289 C-terminal domain [103624] (1)
  1. Hypothetical protein Ta0289 C-terminal domain [103625]
    1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [103626] (1)
Hypothetical protein MTH1184 [57821] (1)
contains two CXC motifs
uperfamily
1. Hypothetical protein MTH1184 [57822] (1)
  possible metal-binding fold
  1. Hypothetical protein MTH1184 [57823]
    1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [57824] (1)
Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain [57825] (1)
uperfamily
1. Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain [57826] (2)
  1. Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain [57827]
    1. Escherichia coli [TaxId: 562] [57828] (59)
      SQ P00478
    2. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [111453] (2)
Zn-binding ribosomal proteins [57829] (8)
uperfamily
1. Ribosomal protein L37ae [57830] (1)
  1. Ribosomal protein L37ae [57831]
    1. Archaeon Haloarcula marismortui [TaxId: 2238] [57832] (58)
      SQ P60619
2. Ribosomal protein L37e [57833] (1)
  1. Ribosomal protein L37e [57834]
    1. Archaeon Haloarcula marismortui [TaxId: 2238] [57835] (40)
      SQ P32410
3. Ribosomal protein L44e [57836] (1)
  1. Ribosomal protein L44e [57837]
    1. Archaeon Haloarcula marismortui [TaxId: 2238] [57838] (40)
      SQ P32411
4. Ribosomal protein S27e [90217] (1)
  1. Ribosomal protein S27e [90218]
    1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [90219] (1)
5. Ribosomal protein L32p [144200] (3)
  Pfam 01783; metal ion-binding site is lost in some members; includes the N-terminal, mainly helical tail
  1. Ribosomal protein L32p [144201]
    1. Escherichia coli [TaxId: 562] [144202] (27)
      SQ P0A7N4 1-56
    2. Thermus thermophilus [TaxId: 274] [161177] (7)
      SQ P80339 1-59
    3. Deinococcus radiodurans [TaxId: 1299] [161178] (10)
      SQ P49228 2-59
6. Ribosomal protein L33p [144203] (3)
  Pfam 00471; corresponds structurally and functionally to the ribosomal L44e from eukaryota and archaea; metal ion-binding site is lost in most members
  1. Ribosomal protein L33p [144204]
    1. Escherichia coli [TaxId: 562] [144205] (9)
      SQ P0A7N9 1-54
    2. Deinococcus radiodurans [TaxId: 1299] [161179] (6)
      SQ Q9RSS4 2-54
    3. Thermus thermophilus [TaxId: 274] [161180] (9)
      SQ P35871 8-52
7. Ribosomal protein L40e [161181] (1)
  Pfam 01020
  1. Ribosomal protein L40e [161182]
    1. Sulfolobus solfataricus [TaxId: 2287] [161183] (1)
      SQ Q980V5 1-56
8. Ribosomal protein S27a [161184] (1)
  Pfam 01599
  1. Ribosomal protein S27ae [161185]
    1. Thermoplasma acidophilum [TaxId: 2303] [161186] (1)
      SQ Q9HJ78 1-55
RNA polymerase subunits [63393] (2)
uperfamily
1. RBP12 subunit of RNA polymerase II [64576] (1)
  1. RBP12 subunit of RNA polymerase II [64577]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64578] (30)
      SQ P40422; part of multichain biological unit
2. RpoE2-like [111454] (1)
  Pfam 04035
  1. putative DNA-directed RNA polymerase subunit E'' (RpoE2) [111455]
    1. Pyrococcus furiosus [TaxId: 2261] [111456] (1)
      SQ Q8U440
NOB1 zinc finger-like [144206] (1)
uperfamily
1. NOB1 zinc finger-like [144207] (1)
  1. RNA-binding protein NOB1 (Nin one binding) [144208]
    1. Mouse (Mus musculus) [TaxId: 10090] [144209] (1)
      SQ Q8BW10 251-316
Nop10-like SnoRNP [144210] (1)
uperfamily
1. Nucleolar RNA-binding protein Nop10-like [144211] (3)
  Pfam 04135; contains N-terminal zinc-finger domain similar to the insert finger of the Initiation factor eIF2 gamma subunit (scop_pr 75204)
  1. H/aca ribonucleoprotein complex subunit 3 [144212]
    lacks the zinc-binding site, mostly unstructured
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [144213] (2)
      SQ Q6Q547 2-58
  2. Ribosome biogenesis protein Nop10 [144214]
    1. Archaeon Pyrococcus furiosus [TaxId: 2261] [144215] (4)
      SQ Q8U1R4 4-55
    2. Archaeon Methanococcus jannaschii [TaxId: 2190] [144216] (2)
      SQ P81303 1-60
CSL zinc finger [144217] (1)
uperfamily
1. CSL zinc finger [144218] (2)
  Pfam 05207
  1. DelGEF-interacting protein 1, DelGIP1 [144219]
    1. Mouse (Mus musculus) [TaxId: 10090] [144220] (1)
      SQ Q8K0W9 1-69
  2. Diphthamide biosynthesis protein 3, DPH3 [144221]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [144222] (2)
      SQ Q3E840 1-82! SQ Q3E840 2-82
YfgJ-like [161187] (1)
duplication: consists of two rubredoxin-like (sub)domains, interlocked together
1. YfgJ-like [161188] (1)
  Pfam 07191, DUF1407
  1. Hypothetical protein YfgJ [161189]
    1. Escherichia coli [TaxId: 562] [161190] (1)
      SQ P76575 13-83