Structural Classification of Proteins

Superfamily: Ribbon-helix-helix

: formerly Met repressor-like; dimeric proteins; the N-termini form a small beta-sheet ribbon
uperfamily

Lineage:

Root: scop
Class: All alpha proteins [46456]
Fold: Ribbon-helix-helix [47597]
core: 4 helices; array of 2 hairpins, opened
Superfamily: Ribbon-helix-helix [47598]
formerly Met repressor-like; dimeric proteins; the N-termini form a small beta-sheet ribbon
uperfamily

Families:

Arc/Mnt-like phage repressors [47599] (2)
1. Arc repressor [47600]
  1. Salmonella bacteriophage P22 [TaxId: 10754] [47601] (12)
    1. 1u9p
      automatically matched to d1arqa_
      1. region a:72-107 [119649]
    2. 1baz
      mutant
      1. chain a [17421]
      2. chain b [17422]
      3. chain c [17423]
      4. chain d [17424]
    3. 1myk
      mutant
      1. chain a [17425]
      2. chain b [17426]
    4. 1myl
      mutant
      1. chain a [17427]
      2. chain b [17428]
      3. chain c [17429]
      4. chain d [17430]
      5. chain e [17431]
      6. chain f [17432]
    5. 1bdt
      protein/DNA complex
      1. chain a [17433]
      2. chain b [17434]
      3. chain c [17435]
      4. chain d [17436]
    6. 1bdv
      protein/DNA complex; mutant
      1. chain a [17441]
      2. chain b [17442]
      3. chain c [17443]
      4. chain d [17444]
    7. 1par
      protein/DNA complex
      1. chain a [17437]
      2. chain b [17438]
      3. chain c [17439]
      4. chain d [17440]
    8. 1arq
      1. chain a [17447]
      2. chain b [17448]
    9. 1arr
      1. chain a [17449]
      2. chain b [17450]
    10. 1qtg
      mutant
      1. chain a [17451]
      2. chain b [17452]
    11. 1b28
      myl mutant
      1. chain a [17445]
      2. chain b [17446]
    12. 1nla
      a mutant with 3(10) helices replacing a wild-type beta-ribbon
      1. chain a [85848]
      2. chain b [85849]
2. Mnt repressor [47602]
  1. Salmonella bacteriophage P22 [TaxId: 10754] [47603] (1)
    1. 1mnt
      includes 15 residues common with the tetramerization domain
      mutant
      1. chain a [17453]
      2. chain b [17454]
CopG-like [100970] (5)
similar to the phage repressor family
1. Transcriptional repressor CopG [47605]
  plasmid-encoded
  1. Streptococcus agalactiae [TaxId: 1311] [47606] (3)
    1. 2cpg
      1. chain a [17455]
      2. chain b [17456]
      3. chain c [17457]
    2. 1ea4
      1. chain a [64861]
      2. chain b [64862]
      3. chain d [64863]
      4. chain e [64864]
      5. chain f [64865]
      6. chain g [64866]
      7. chain h [64867]
      8. chain j [64868]
      9. chain k [64869]
      10. chain l [64870]
    3. 1b01
      1. chain a [17458]
      2. chain b [17459]
2. Plasmid partition protein ParG [101203]
  1. Salmonella enterica [TaxId: 28901] [101204] (1)
    1. 1p94
      1. chain a [94380]
      2. chain b [94381]
3. Nickel responsive regulator NikR, N-terminal domain [101205]
  1. Escherichia coli [TaxId: 562] [101206] (11)
    1. 2hza
      automatically matched to d1q5va1
      complexed with 3cm, ni
      1. region a:1-48 [136907]
    2. 2hza
      automatically matched to d1q5va1
      complexed with 3cm, ni
      1. region b:1-43 [136909]
    3. 1q5v
      1. region a:1-48 [95937]
      2. region b:1-48 [95939]
      3. region c:1-48 [95941]
      4. region d:1-48 [95943]
    4. 2hzv
      automatically matched to d1q5va1
      complexed with k, ni
      1. region a:1-48 [136916]
    5. 2hzv
      automatically matched to d1q5va1
      complexed with k, ni
      1. region b:1-48 [136918]
    6. 2hzv
      automatically matched to d1q5va1
      complexed with k, ni
      1. region c:1-48 [136920]
    7. 2hzv
      automatically matched to d1q5va1
      complexed with k, ni
      1. region d:1-48 [136922]
    8. 2hzv
      automatically matched to d1q5va1
      complexed with k, ni
      1. region e:1-48 [136924]
    9. 2hzv
      automatically matched to d1q5va1
      complexed with k, ni
      1. region f:1-48 [136926]
    10. 2hzv
      automatically matched to d1q5va1
      complexed with k, ni
      1. region g:1-48 [136928]
    11. 2hzv
      automatically matched to d1q5va1
      complexed with k, ni
      1. region h:1-48 [136930]
  2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [140543] (12)
    SQ O58316 1-50
    1. 2bj7
      automatically matched to 2BJ1 A:1-50
      complexed with cl, edo, ni, pg4
      1. region a:1-50 [128608]
    2. 2bj7
      automatically matched to 2BJ1 A:1-50
      complexed with cl, edo, ni, pg4
      1. region b:1-50 [128610]
    3. 2bj8
      automatically matched to 2BJ1 A:1-50
      complexed with cl, edo, epe, ni, pg4
      1. region a:1-50 [128612]
    4. 2bj8
      automatically matched to 2BJ1 A:1-50
      complexed with cl, edo, epe, ni, pg4
      1. region b:1-50 [128614]
    5. 2bj3
      automatically matched to 2BJ1 A:1-50
      complexed with cl, mg
      1. region a:1-50 [128600]
    6. 2bj3
      automatically matched to 2BJ1 A:1-50
      complexed with cl, mg
      1. region b:2-50 [128602]
    7. 2bj3
      automatically matched to 2BJ1 A:1-50
      complexed with cl, mg
      1. region c:1-50 [128604]
    8. 2bj3
      automatically matched to 2BJ1 A:1-50
      complexed with cl, mg
      1. region d:2-50 [128606]
    9. 2bj9
      automatically matched to 2BJ1 A:1-50
      complexed with ni, pg4, po4
      1. region a:1-50 [128616]
    10. 2bj9
      automatically matched to 2BJ1 A:1-50
      complexed with ni, pg4, po4
      1. region b:1-50 [128618]
    11. 2bj1
      complexed with cl, ni
      1. region a:1-50 [128596]
    12. 2bj1
      automatically matched to 2BJ1 A:1-50
      complexed with cl, ni
      1. region b:1-50 [128598]
4. Uncharacterized protein HP0222 [158480]
  1. Helicobacter pylori [TaxId: 210] [158481] (2)
    SQ O25010 31-73
    1. 1x93
      1. region a:31-73 [145859]
    2. 1x93
      automatically matched to 1X93 A:31-73
      1. region b:31-73 [145860]
Omega transcriptional repressor [100971] (1)
plasmid-encoded, similar to the phage repressor family
1. Omega transcriptional repressor [69031]
  1. Streptococcus pyogenes [TaxId: 1314] [69032] (13)
    1. 1irq
      1. chain a [66297]
      2. chain b [66298]
    2. 2bnw
      automatically matched to d1irqb_
      1. region a:23-71 [128857]
    3. 2bnw
      automatically matched to d1irqb_
      1. region b:23-71 [128858]
    4. 2bnw
      automatically matched to d1irqb_
      1. region c:23-71 [128859]
    5. 2bnw
      automatically matched to d1irqb_
      1. region d:25-71 [128860]
    6. 2bnz
      automatically matched to d1irqb_
      1. region a:23-71 [128863]
    7. 2bnz
      automatically matched to d1irqb_
      1. region b:23-71 [128864]
    8. 2bnz
      automatically matched to d1irqb_
      1. region c:23-71 [128865]
    9. 2bnz
      automatically matched to d1irqb_
      1. region d:25-71 [128866]
    10. 2cax
      automatically matched to d1irqb_
      1. region a:23-71 [130163]
    11. 2cax
      automatically matched to d1irqb_
      1. region b:23-71 [130164]
    12. 2cax
      automatically matched to d1irqb_
      1. region c:23-71 [130165]
    13. 2cax
      automatically matched to d1irqb_
      1. region d:25-71 [130166]
Met repressor, MetJ (MetR) [100972] (1)
1. Met repressor, MetJ (MetR) [47607]
  1. Escherichia coli [TaxId: 562] [47608] (10)
    1. 1cmc
      complexed with mg, sam
      1. chain a [17462]
      2. chain b [17463]
    2. 1cmb
      complexed with po4
      1. chain a [17460]
      2. chain b [17461]
    3. 1mjk
      complexed with po4; mutant
      1. chain a [17464]
      2. chain b [17465]
    4. 1mjl
      complexed with sam; mutant
      1. chain a [17470]
      2. chain b [17471]
    5. 1mjo
      protein/DNA complex; complexed with ca, sam; mutant
      1. chain a [17466]
      2. chain b [17467]
      3. chain c [17468]
      4. chain d [17469]
    6. 1mjm
      protein/DNA complex; mutant
      1. chain a [17472]
      2. chain b [17473]
    7. 1mj2
      protein/DNA complex; complexed with ca, sam; mutant
      1. chain a [17474]
      2. chain b [17475]
      3. chain c [17476]
      4. chain d [17477]
    8. 1mjq
      protein/DNA complex; complexed with sam; mutant
      1. chain a [17478]
      2. chain b [17479]
      3. chain c [17480]
      4. chain d [17481]
      5. chain g [17482]
      6. chain h [17483]
      7. chain i [17484]
      8. chain j [17485]
    9. 1cma
      protein/DNA complex; complexed with sam
      1. chain a [17486]
      2. chain b [17487]
    10. 1mjp
      protein/DNA complex; mutant
      1. chain a [17488]
      2. chain b [17489]
NE0241-like [140544] (1)
contains extra C-terminal long helix; currently consists of an orphan protein
1. Hypothetical protein NE0241 [140545]
  1. Nitrosomonas europaea [TaxId: 915] [140546] (1)
    SQ Q82XL7 10-95
    1. 1zx3
      1. region a:10-95 [125762]
SeqA N-terminal domain-like [140547] (1)
N-terminal part of Pfam 03925
1. SeqA [140548]
  a negative modulator of replication initiation
  1. Escherichia coli [TaxId: 562] [140549] (4)
    SQ P0AFY8 1-35
    1. 1xrx
      complexed with ca
      1. region a:1-35 [122264]
    2. 1xrx
      automatically matched to 1XRX A:1-35
      complexed with ca
      1. region b:1-35 [122265]
    3. 1xrx
      automatically matched to 1XRX A:1-35
      complexed with ca
      1. region c:1-35 [122266]
    4. 1xrx
      automatically matched to 1XRX A:1-35
      complexed with ca
      1. region d:1-35 [122267]
Trafficking protein A-like [140550] (1)
1. Trafficking protein A [140551]
  1. Neisseria gonorrhoeae [TaxId: 485] [140552] (8)
    SQ Q5F881 2-70
    1. 2bsq
      complexed with 5iu; mutant
      1. region e:2-70 [129102]
    2. 2bsq
      automatically matched to 2BSQ E:2-70
      complexed with 5iu; mutant
      1. region f:2-66 [129103]
    3. 2bsq
      automatically matched to 2BSQ E:2-70
      complexed with 5iu; mutant
      1. region g:2-69 [129104]
    4. 2bsq
      automatically matched to 2BSQ E:2-70
      complexed with 5iu; mutant
      1. region h:2-65 [129105]
    5. 2h1o
      complexed with 5iu; mutant
      1. region e:2-69 [145278]
    6. 2h1o
      automatically matched to 2H1O E:2-69
      complexed with 5iu; mutant
      1. region f:2-65 [145279]
    7. 2h1o
      automatically matched to 2H1O E:2-69
      complexed with 5iu; mutant
      1. region g:2-68 [145280]
    8. 2h1o
      automatically matched to 2H1O E:2-69
      complexed with 5iu; mutant
      1. region h:2-64 [145281]
VCA0319-like [140553] (1)
COG4453; extended and extra C-terminal helices; potential component of the bi-partite system also including an acetyltransferase
1. Hypothetical protein VCA0482 (VCA0319) [140554]
  Proteins of identical sequence, VCA0482 VCA0319 are encoded by two different genes
  1. Vibrio cholerae [TaxId: 666] [140555] (2)
    SQ Q9K2J6 3-83
    1. 1y9b
      1. region a:3-83 [122777]
    2. 1y9b
      automatically matched to 1Y9B A:3-83
      1. region b:6-83 [122778]
VirC2-like [158482] (1)
Pfam 07181; duplicated ribbon-helix-helix motif; fold forms a trefoil knot
1. VirC2 [158483]
  Encoded by Ti plasmid
  1. Agrobacterium tumefaciens [TaxId: 358] [158484] (1)
    SQ P07166 82-202
    1. 2rh3
      1. region a:82-202 [152027]
PutA pre-N-terminal region-like [158485] (1)
in PutA it forms a separate ribbon-helix-helix domain connected to the N-terminal enzymatic domain by a flexible linker
1. Bifunctional protein putA [158486]
  1. Escherichia coli [TaxId: 562] [158487] (6)
    SQ P09546 3-45
    1. 2ay0
      complexed with cl; mutant
      1. region a:3-45 [146077]
    2. 2ay0
      automatically matched to 2AY0 A:3-45
      complexed with cl; mutant
      1. region b:3-44 [146078]
    3. 2ay0
      automatically matched to 2AY0 A:3-45
      complexed with cl; mutant
      1. region c:3-45 [146079]
    4. 2ay0
      automatically matched to 2AY0 A:3-45
      complexed with cl; mutant
      1. region d:3-45 [146080]
    5. 2ay0
      automatically matched to 2AY0 A:3-45
      complexed with cl; mutant
      1. region e:3-45 [146081]
    6. 2ay0
      automatically matched to 2AY0 A:3-45
      complexed with cl; mutant
      1. region f:3-45 [146082]
MJ0366-like [158488] (1)
PfamB 022101; duplicated ribbon-helix-helix motif; forms trefoil knot; predicted DNA binding
1. Uncharacterized protein MJ0366 [158489]
  1. Methanococcus jannaschii [TaxId: 2190] [158490] (1)
    SQ Q57812 6-87
    1. 2efv
      complexed with po4
      1. region a:6-87 [146819]