Summary: Single-strand binding protein family
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Single-stranded binding protein Edit Wikipedia article
| SSB | |||||||||
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Crystal structure of PriB- a primosomal DNA replication protein of Escherichia coli
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| Identifiers | |||||||||
| Symbol | SSB | ||||||||
| Pfam | PF00436 | ||||||||
| Pfam clan | CL0021 | ||||||||
| InterPro | IPR000424 | ||||||||
| PROSITE | PDOC00602 | ||||||||
| SCOP | 1kaw | ||||||||
| SUPERFAMILY | 1kaw | ||||||||
| TCDB | 3.A.7 | ||||||||
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Single-stranded binding proteins (SSBs) are a class of proteins that have been identified in both viruses and organisms from bacteria to humans.
Contents
Function
Binds to single-stranded DNA and prevents annealing of single-stranded DNA into double-stranded DNA, also prevents single strand DNA from degradation.
Viral SSB
| Viral_DNA_bp | |||||||||
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Single stranded DNA-binding protein(icp8) from herpes simplex virus-1
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| Identifiers | |||||||||
| Symbol | Viral_DNA_bp | ||||||||
| Pfam | PF00747 | ||||||||
| InterPro | IPR000635 | ||||||||
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Although the overall picture of human cytomegalovirus (HHV-5) DNA synthesis appears typical of the herpesviruses, some novel features are emerging.
Structure
In ICP8, the herpes simplex virus (HSV-1) single-strand DNA-binding protein (ssDNA-binding protein (SSB)), the head consists of the eight alpha helices. The front side of the neck region consists of a five-stranded beta-sheet and two alpha helices, whereas the back side is a three-stranded beta-sheet The shoulder part of the N-terminal domain contains an alpha-helical and beta-sheet region.[1] The herpes simplex virus (HSV-1) SSB, ICP8, is a nuclear protein that, along other replication proteins is required for viral DNA replication during lytic infection.[1]
Mechanism
Six herpes virus-group-common genes encode proteins that likely constitute the replication fork machinery, including a two-subunit DNA polymerase, a Helicase-primase complex and a single-stranded DNA-binding protein.[2] The human herpesvirus 1 (HHV-1) single-strand DNA-binding protein ICP8 is a 128kDa zinc metalloprotein. Photoaffinity labeling has shown that the region encompassing amino acid residues 368-902 contains the single-strand DNA-binding site of ICP8.[3] The HHHV-1 UL5, UL8, and UL52 genes encode an essential heterotrimeric DNA helicase-primase that is responsible for concomitant DNA unwinding and primer synthesis at the viral DNA replication fork. ICP8 may stimulate DNA unwinding and enable bypass of cisplatin damaged DNA by recruiting the helicase-primase to the DNA.[4]
Bacterial SSB
SSB protein domains in bacteria are important maintaining DNA metabolism, more specifically DNA replication, repair and recombination.[5] It has a structure of three beta-strands to a single six-stranded beta-sheet to form a dimer.[6]
Eukaryotic replication protein A
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Replication protein A
(heterotrimer) |
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| This is an image of human Replication protein A. From PDB: 1L1O Proteopedia protein A Replication protein A | ||
| Subunit name |
Gene | Chromosomal locus |
| Replication protein A1 | RPA1 | Chr. 17 p13.3 |
| Replication protein A2 | RPA2 | Chr. 1 p35.3 |
| Replication protein A3 | RPA3 | Chr. 7 p21.3 |
Replication protein A is the functional equivalent of SSB in the nucleus of eukaryotic cells, though there is no sequence homology.
Eukaryotic mitochondrial SSB
The mitochondria of eukaryotic cells contain their own single stranded DNA binding protein. Human mitochondrial SSB (mtSSB) binds to single-stranded mitochondrial DNA as a tetramer and has sequence similarity to bacterial SSB.[7] Human mtSSB is encoded by the SSBP1 gene. In yeast, it is encoded by the RIM1 gene.[8]
See also
References
- ^ a b Mapelli M, Panjikar S, Tucker PA (2005). "The crystal structure of the herpes simplex virus 1 ssDNA-binding protein suggests the structural basis for flexible, cooperative single-stranded DNA binding". J Biol Chem. 280 (4): 2990–7. doi:10.1074/jbc.M406780200. PMID 15507432.
- ^ Anders DG, McCue LA (1996). "The human cytomegalovirus genes and proteins required for DNA synthesis". Intervirology. 39 (5–6): 378–88. doi:10.1159/000150508. PMID 9130047.
- ^ White EJ, Boehmer PE (October 1999). "Photoaffinity labeling of the herpes simplex virus type-1 single-strand DNA-binding protein (ICP8) with oligodeoxyribonucleotides". Biochem. Biophys. Res. Commun. 264 (2): 493–7. doi:10.1006/bbrc.1999.1566. PMID 10529391.
- ^ Tanguy Le Gac N, Villani G, Boehmer PE (May 1998). "Herpes simplex virus type-1 single-strand DNA-binding protein (ICP8) enhances the ability of the viral DNA helicase-primase to unwind cisplatin-modified DNA". J. Biol. Chem. 273 (22): 13801–7. doi:10.1074/jbc.273.22.13801. PMID 9593724.
- ^ Meyer RR, Laine PS (December 1990). "The single-stranded DNA-binding protein of Escherichia coli". Microbiol. Rev. 54 (4): 342–80. PMC 372786
. PMID 2087220. - ^ Raghunathan S, Ricard CS, Lohman TM, Waksman G (June 1997). "Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution". Proc. Natl. Acad. Sci. U.S.A. 94 (13): 6652–7. doi:10.1073/pnas.94.13.6652. PMC 21213 . PMID 9192620.
- ^ Tiranti, V; Rocchi, M; DiDonato, S; Zeviani, M (30 April 1993). "Cloning of human and rat cDNAs encoding the mitochondrial single-stranded DNA-binding protein (SSB)". Gene. 126 (2): 219–25. doi:10.1016/0378-1119(93)90370-i. PMID 8482537.
- ^ Van Dyck, E; Foury, F; Stillman, B; Brill, SJ (September 1992). "A single-stranded DNA binding protein required for mitochondrial DNA replication in S. cerevisiae is homologous to E. coli SSB". The EMBO Journal. 11 (9): 3421–30. PMC 556877 . PMID 1324172.
This article incorporates text from the public domain Pfam and InterPro IPR000635
External links
- Single-Stranded DNA Binding Proteins at the US National Library of Medicine Medical Subject Headings (MeSH)
- SSB in PFAM[permanent dead link]
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Single-strand binding protein family Provide feedback
This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA.
Literature references
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Raghunathan S, Ricard CS, Lohman TM, Waksman G; , Proc Natl Acad Sci U S A 1997;94:6652-6657.: Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution. PUBMED:9192620 EPMC:9192620
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Yang C, Curth U, Urbanke C, Kang C; , Nat Struct Biol 1997;4:153-157.: Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 A resolution. PUBMED:9033597 EPMC:9033597
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Webster G, Genschel J, Curth U, Urbanke C, Kang C, Hilgenfeld R; , FEBS Lett 1997;411:313-316.: A common core for binding single-stranded DNA: structural comparison of the single-stranded DNA-binding proteins (SSB) from E. coli and human mitochondria. PUBMED:9271227 EPMC:9271227
Internal database links
| SCOOP: | DUF3217 Phage_SSB tRNA_anti-codon tRNA_anti_2 |
| Similarity to PfamA using HHSearch: | tRNA_anti-codon |
External database links
| HOMSTRAD: | SSB |
| PROSITE: | PDOC00602 |
| SCOP: | 1kaw |
| Transporter classification: | 3.A.7 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000424
The Escherichia coli single-strand binding protein [PUBMED:2087220] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterized in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.
Primosomal replication protein N (PriB) is a specialist protein from bacteria that binds single-stranded DNA at the primosome assembly site (PAS). The primosome is a mobile multiprotein replication priming complex which is believe to operate on the lagging-strand template at the E. coli DNA replication fork [PUBMED:1856227]. The primosome consists of one monomer of PriC and DnaT, two monomers of PriA, two dimers of PriB and one hexamer of DnaB [PUBMED:8663106].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Molecular function | single-stranded DNA binding (GO:0003697) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan OB (CL0021), which has the following description:
The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin [1]. 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 [1].
The clan contains the following 107 members:
BOF BRCA-2_OB1 BRCA-2_OB3 CcmE CDC13_N Cdc13_OB2 CDC24_OB1 CDC24_OB2 CDC24_OB3 CSD CSD2 CusF_Ec CysA_C_terminal DNA_ligase_A_C DNA_ligase_C DNA_ligase_OB DNA_ligase_OB_2 DNA_pol_D_N DUF1344 DUF1449 DUF2110 DUF223 DUF2815 DUF3127 DUF3217 DUF3299 DUF4539 DUF961 EFP eIF-1a eIF-5a Elong-fact-P_C EutN_CcmL EXOSC1 FbpC_C_terminal Fimbrial_PilY2 GlcV_C_terminal Gp138_N gp32 HIN ID MCM_OB mRNA_cap_C MRP-S35 NfeD NigD_N NlpE_C OB_aCoA_assoc OB_Dis3 OB_MalK OB_NTP_bind OB_RNB PCB_OB Phage_DNA_bind Phage_SSB Pol_alpha_B_N POT1 POT1PC Prot_ATP_ID_OB Prot_ATP_OB_N RecG_wedge RecJ_OB 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 Ribosomal_S4e RMI1_C RMI1_N RMI2 RNA_pol_Rbc25 RNA_pol_Rpb8 RNA_pol_RpbG RNase_II_C_S1 RPA43_OB Rrp44_CSD1 Rrp44_S1 RsgA_N RuvA_N S1 S1-like S1_2 SfsA_N SSB ssDBP Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TPP1 TRAM TRAM_2 tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind TTC5_OBAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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| Seed (52) |
Full (16249) |
Representative proteomes | UniProt (45741) |
NCBI (56291) |
Meta (2774) |
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| RP15 (4309) |
RP35 (11091) |
RP55 (16446) |
RP75 (23203) |
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| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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| Seed (52) |
Full (16249) |
Representative proteomes | UniProt (45741) |
NCBI (56291) |
Meta (2774) |
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|---|---|---|---|---|---|---|---|---|---|
| RP15 (4309) |
RP35 (11091) |
RP55 (16446) |
RP75 (23203) |
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| Raw Stockholm | |||||||||
| Gzipped | |||||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
| Seed source: | Prosite & COG2965 |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Finn RD  , Bateman A
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| Number in seed: | 52 |
| Number in full: | 16249 |
| Average length of the domain: | 102.90 aa |
| Average identity of full alignment: | 29 % |
| Average coverage of the sequence by the domain: | 64.16 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 104 | ||||||||||||
| Family (HMM) version: | 25 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
Archea
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Eukaryota
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Bacteria
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Viruses
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Unclassified sequence
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Interactions
There is 1 interaction for this family. More...
SSBStructures
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 SSB domain has been found. There are 133 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 sequence.
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