Summary: Zinc-binding domain of primase-helicase
Zinc-binding domain of primase-helicase Provide feedback
No Pfam abstract.
Kato M, Ito T, Wagner G, Richardson CC, Ellenberger T; , Mol Cell 2003;11:1349-1360.: Modular architecture of the bacteriophage T7 primase couples RNA primer synthesis to DNA synthesis. PUBMED:12769857 EPMC:12769857
Internal database links
|Similarity to PfamA using HHSearch:||TF_Zn_Ribbon RRN7|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR013237
This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [PUBMED:8253092, PUBMED:9185573, PUBMED:10892646].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||DNA primase activity (GO:0003896)|
|zinc ion binding (GO:0008270)|
|helicase activity (GO:0004386)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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A clan of zinc-binding ribbon domains.
The clan contains the following 50 members:A2L_zn_ribbon Auto_anti-p27 Baculo_LEF5_C DNA_RNApol_7kD DUF1610 DUF1936 DUF2116 DUF2180 DUF2387 DZR Elf1 GATA NinF NOB1_Zn_bind Ogr_Delta OrfB_Zn_ribbon PhnA_Zn_Ribbon Prim_Zn_Ribbon Ribosomal_L32p Ribosomal_L37ae Ribosomal_S27 Ribosomal_S27e RNA_POL_M_15KD RRN7 Spt4 TF_Zn_Ribbon TFIIS_C Tnp_zf-ribbon_2 Topo_Zn_Ribbon Toprim_Crpt Trm112p UPF0547 zf-C4_Topoisom zf-CHC2 zf-DHHC zf-dskA_traR zf-FPG_IleRS zf-GRF zf-NADH-PPase zf-RanBP zf-ribbon_3 zf-TFIIB zinc-ribbons_6 zinc_ribbon_2 zinc_ribbon_4 zinc_ribbon_5 Zn-ribbon_8 Zn_ribbon_recom Zn_Tnp_IS1 Zn_Tnp_IS1595
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Seed source:||Pfam-B_18441 (release 17.0)|
|Number in seed:||18|
|Number in full:||651|
|Average length of the domain:||37.60 aa|
|Average identity of full alignment:||54 %|
|Average coverage of the sequence by the domain:||6.24 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|Download:||download the raw HMM for this family|
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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 Prim_Zn_Ribbon domain has been found. There are 2 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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