Summary: Oligonucleotide/oligosaccharide-binding (OB)-fold
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Oligonucleotide/oligosaccharide-binding (OB)-fold Provide feedback
This family is found towards the C-terminus of the DEAD-box helicases (PF00270). In these helicases it is apparently always found in association with PF04408. There do seem to be a couple of instances where it occurs by itself - e.g. Q84VZ2. The structure PDB:3i4u adopts an OB-fold. helicases (PF00270). In these helicases it is apparently always found in association with PF04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins .
Walbott H, Mouffok S, Capeyrou R, Lebaron S, Humbert O, van Tilbeurgh H, Henry Y, Leulliot N;, EMBO J. 2010;29:2194-2204.: Prp43p contains a processive helicase structural architecture with a specific regulatory domain. PUBMED:20512115 EPMC:20512115
Kim T, Pazhoor S, Bao M, Zhang Z, Hanabuchi S, Facchinetti V, Bover L, Plumas J, Chaperot L, Qin J, Liu YJ;, Proc Natl Acad Sci U S A. 2010; [Epub ahead of print]: Aspartate-glutamate-alanine-histidine box motif (DEAH)/RNA helicase A helicases sense microbial DNA in human plasmacytoid dendritic cells. PUBMED:20696886 EPMC:20696886
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The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin . The common part of the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands .
The clan contains the following 70 members:BOF BRCA-2_OB1 BRCA-2_OB3 CDC24_OB1 CDC24_OB2 CDC24_OB3 CSD CusF_Ec DNA_ligase_A_C DNA_ligase_OB DNA_ligase_OB_2 DUF1344 DUF2110 DUF223 DUF3127 DUF4539 EFP eIF-1a eIF-5a Elong-fact-P_C EutN_CcmL EXOSC1 MCM_OB mRNA_cap_C MRP-S35 NigD_N NlpE_C OB_aCoA_assoc OB_NTP_bind OB_RNB PCB_OB Phage_DNA_bind POT1 Prot_ATP_ID_OB RecG_wedge RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rep_fac-A_C REPA_OB_2 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 Ribosomal_S28e RMI2 RNA_pol_Rbc25 RNA_pol_Rpb8 RNA_pol_RpbG Rrp44_CSD1 Rrp44_S1 RsgA_N RuvA_N S1 S1-like S1_2 SSB Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TRAM tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Yeats C|
|Number in seed:||58|
|Number in full:||9140|
|Average length of the domain:||84.20 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||8.24 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the OB_NTP_bind domain has been found. There are 11 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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