Fold: Rubredoxin-like

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

Lineage:

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

Superfamilies:

1. 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
2. Microbial and mitochondrial ADK, insert "zinc finger" domain [57774] (1)
   uperfamily
   1. Microbial and mitochondrial ADK, insert "zinc finger" domain [57775] (8)
3. NADH pyrophosphatase intervening domain [116738] (1)
   uperfamily
   1. NADH pyrophosphatase intervening domain [116739] (1)
4. Zinc beta-ribbon [57783] (5)
   uperfamily
   1. Transcriptional factor domain [57784] (6)
   2. DNA primase zinc finger [57792] (2)
      contains alpha-helices in the N- and C-terminal extensions (linkers?)
   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
   4. Putative zinc binding domain [118285] (1)
      Pfam 05129; DUF701
   5. PhnA zinc-binding domain [144191] (1)
      Pfam 08274
5. 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?)
6. Rubredoxin-like [57802] (3)
   uperfamily
   1. Rubredoxin [57803] (10)
   2. Desulforedoxin [57813] (3)
   3. Cytochrome c oxidase Subunit F [57818] (1)
      membrane-anchored rubredoxin-like domain
7. Zn-finger domain of Sec23/24 [82919] (1)
   uperfamily
   1. Zn-finger domain of Sec23/24 [82920] (2)
8. 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)
9. 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)
10. Hypothetical protein MTH1184 [57821] (1)
    contains two CXC motifs
    uperfamily
    1. Hypothetical protein MTH1184 [57822] (1)
       possible metal-binding fold
11. Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain [57825] (1)
    uperfamily
    1. Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain [57826] (2)
12. Zn-binding ribosomal proteins [57829] (8)
    uperfamily
    1. Ribosomal protein L37ae [57830] (1)
    2. Ribosomal protein L37e [57833] (1)
    3. Ribosomal protein L44e [57836] (1)
    4. Ribosomal protein S27e [90217] (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
    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
    7. Ribosomal protein L40e [161181] (1)
       Pfam 01020
    8. Ribosomal protein S27a [161184] (1)
       Pfam 01599
13. RNA polymerase subunits [63393] (2)
    uperfamily
    1. RBP12 subunit of RNA polymerase II [64576] (1)
    2. RpoE2-like [111454] (1)
       Pfam 04035
14. NOB1 zinc finger-like [144206] (1)
    uperfamily
    1. NOB1 zinc finger-like [144207] (1)
15. 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)
16. CSL zinc finger [144217] (1)
    uperfamily
    1. CSL zinc finger [144218] (2)
       Pfam 05207
17. YfgJ-like [161187] (1)
    duplication: consists of two rubredoxin-like (sub)domains, interlocked together
    1. YfgJ-like [161188] (1)
       Pfam 07191, DUF1407

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