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7  structures 1034  species 0  interactions 1223  sequences 42  architectures

Family: ORC4_C (PF14629)

Summary: Origin recognition complex (ORC) subunit 4 C-terminus

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "ORC4". More...

ORC4 Edit Wikipedia article

ORC4
Identifiers
AliasesORC4, ORC4L, ORC4P, origin recognition complex subunit 4
External IDsOMIM: 603056 MGI: 1347043 HomoloGene: 8059 GeneCards: ORC4
Gene location (Human)
Chromosome 2 (human)
Chr.Chromosome 2 (human)[1]
Chromosome 2 (human)
Genomic location for ORC4
Genomic location for ORC4
Band2q23.1Start147,930,397 bp[1]
End148,021,604 bp[1]
RNA expression pattern
PBB GE ORC4L 203351 s at fs.png

PBB GE ORC4L 203352 at fs.png
More reference expression data
Orthologs
SpeciesHumanMouse
Entrez

5000

26428

Ensembl

ENSG00000115947

ENSMUSG00000026761

UniProt

O43929

O88708

RefSeq (mRNA)

NM_001177313
NM_011958
NM_001355296

RefSeq (protein)

NP_001170784
NP_036088
NP_001342225

Location (UCSC)Chr 2: 147.93 – 148.02 MbChr 2: 48.9 – 48.95 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Origin recognition complex subunit 4 is a protein that in humans is encoded by the ORC4 (ORC4L) gene.[5][6][7]

Function

The origin recognition complex (ORC) is a highly conserved six subunit protein complex essential for the initiation of the DNA replication in eukaryotic cells. Studies in yeast demonstrated that ORC binds specifically to origins of replication and serves as a platform for the assembly of additional initiation factors such as Cdc6 and Mcm proteins. The protein encoded by this gene is a subunit of the ORC complex. It has been shown to form a core complex with ORC2L, -3L, and -5L. Three alternatively spliced transcript variants encoding the same protein have been reported.[7]

Interactions

ORC4 has been shown to interact with:

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000115947 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000026761 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ a b Quintana DG, Hou ZH, Thome KC, Hendricks M, Saha P, Dutta A (Nov 1997). "Identification of HsORC4, a member of the human origin of replication recognition complex". The Journal of Biological Chemistry. 272 (45): 28247–51. doi:10.1074/jbc.272.45.28247. PMID 9353276.
  6. ^ Eki T, Dean FB, Kohda A, Okumura K, Abe M, Murakami Y, Ishiai M, Satomoto K, Hurwitz J, O'Donnell M, Hanaoka F (October 1998). "Assignment of the homologue of the yeast origin recognition complex subunit ORC4 (ORC4L) to human chromosome band 2q22-->q23 by in situ hybridization and somatic cell hybrid analysis". Cytogenetics and Cell Genetics. 81 (1): 89–90. doi:10.1159/000014997. PMID 9691185.
  7. ^ a b "Entrez Gene: ORC4L origin recognition complex, subunit 4-like (yeast)".
  8. ^ a b c d e f g h Kneissl M, Pütter V, Szalay AA, Grummt F (Mar 2003). "Interaction and assembly of murine pre-replicative complex proteins in yeast and mouse cells". Journal of Molecular Biology. 327 (1): 111–28. doi:10.1016/s0022-2836(03)00079-2. PMID 12614612.
  9. ^ a b c Dhar SK, Delmolino L, Dutta A (Aug 2001). "Architecture of the human origin recognition complex". The Journal of Biological Chemistry. 276 (31): 29067–71. doi:10.1074/jbc.M103078200. PMID 11395502.
  10. ^ a b Vashee S, Simancek P, Challberg MD, Kelly TJ (Jul 2001). "Assembly of the human origin recognition complex". The Journal of Biological Chemistry. 276 (28): 26666–73. doi:10.1074/jbc.M102493200. PMID 11323433.
  11. ^ Pinto S, Quintana DG, Smith P, Mihalek RM, Hou ZH, Boynton S, Jones CJ, Hendricks M, Velinzon K, Wohlschlegel JA, Austin RJ, Lane WS, Tully T, Dutta A (May 1999). "latheo encodes a subunit of the origin recognition complex and disrupts neuronal proliferation and adult olfactory memory when mutant". Neuron. 23 (1): 45–54. doi:10.1016/s0896-6273(00)80752-7. PMID 10402192.
  12. ^ Quintana DG, Thome KC, Hou ZH, Ligon AH, Morton CC, Dutta A (Oct 1998). "ORC5L, a new member of the human origin recognition complex, is deleted in uterine leiomyomas and malignant myeloid diseases". The Journal of Biological Chemistry. 273 (42): 27137–45. doi:10.1074/jbc.273.42.27137. PMID 9765232.

Further reading

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This is the Wikipedia entry entitled "Origin recognition complex". More...

Origin recognition complex Edit Wikipedia article

Origin recognition complex subunit 2
Identifiers
SymbolORC2
PfamPF04084
InterProIPR007220
Origin recognition complex (ORC) subunit 3 N-terminus
Identifiers
SymbolORC3_N
PfamPF07034
InterProIPR010748
Origin recognition complex subunit 6 (ORC6)
Identifiers
SymbolORC6
PfamPF05460
InterProIPR008721

In molecular biology, origin recognition complex (ORC) is a multi-subunit DNA binding complex (6 subunits) that binds in all eukaryotes and archaea in an ATP-dependent manner to origins of replication. The subunits of this complex are encoded by the ORC1, ORC2, ORC3, ORC4, ORC5 and ORC6 genes.[1][2][3] ORC is a central component for eukaryotic DNA replication, and remains bound to chromatin at replication origins throughout the cell cycle.[4]

ORC directs DNA replication throughout the genome and is required for its initiation.[5][6][7] ORC bound at replication origins serves as the foundation for assembly of the pre-replication complex (pre-RC), which includes Cdc6, Tah11 (a.k.a. Cdt1), and the Mcm2-Mcm7 complex.[8][9][10] Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase.[11][12][13] Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase.[4][14][15][16]

The ORC is present throughout the cell cycle bound to replication origins, but is only active in late mitosis and early G1.

In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR).[5][6][7] ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers.[7][17][18]

Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity.[19] The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability.[10] The ATPase activity of Orc1 is involved in formation of the pre-RC.[20][21][22] ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed.[23] Interactions within ORC suggest that Orc2-3-6 may form a core complex.[4]

Proteins

This process was initiated by the loading of Mcm2-7 onto the chromatid by the ORC and associated proteins

The following proteins are present in the ORC:

ORC Protein Subunits, orthology and nomenclature by species[24]
S. cerevisiae S. pombe D. melanogaster Vertebrates
ORC 1-6 ORC 1-6 ORC 1-6 ORC 1-6
Cdc6 Cdc18 Cdc6 Cdc6
Cdt1/Tah11/Sid2 Cdt1 DUP Cdt1/RLF-B
Mcm2 Mcm2/Cdc19/Nda1 Mcm2 Mcm2
Mcm3 Mcm3 Mcm3 Mcm3
Cdc54/Mcm4 Cdc21 DPA Mcm4
Cdc46/Mcm5 Mcm5/Nda4 Mcm5 Mcm5
Mcm6 Mcm6/Mis5 Mcm6 Mcm6
Cdc47/Mcm7 Mcm7 Mcm7 mcm7

Archaea feature a simplified version of the ORC, Mcm, and as a consequence the combined pre-RC. Instead of using six different mcm proteins to form a pseudo-symmetrical heterohexamer, all six subunits in the archaeal MCM are the same. They usually have multiple proteins that are homologous to both Cdc6 and Orc1, some of which perform the function of both. Unlike eukaryotic Orc, they do not always form a complex. In fact, they have divergent complex structures when these do form. Sulfolobus islandicus also uses a Cdt1 homologue to recognize one of its replication origins.[25]

Autonomously replicating sequences

Budding yeast

Autonomously Replicating Sequences (ARS), first discovered in budding yeast, are integral to the success of the ORC. These 100-200bp sequences facilitate replication activity during S phase. ARSs can be placed at any novel location of the chromosomes of budding yeast and will facilitate replication from those sites. A highly conserved sequence of 11bp (known as the A element) is thought to be essential for origin function in budding yeast.[24] The ORC was originally identified by its ability to bind to the A element of the ARS in budding yeast.

Animals

Animal cells contain a much more cryptic version of an ARS, with no conserved sequences found as of yet. However, in animal cells, replication origins gather into bundles called replicon clusters. Each cluster's replicons are similar in length, but individual clusters have replicons of varying length. These replicons all have similar basic residues to which the ORC binds, which in many ways mimic the conserved 11bp A element. All of these clusters are simultaneously activated during S phase.[24]

Role in pre-RC assembly

The ORC is essential for the loading of MCM complexes (Pre-RC) onto DNA. This process is dependent on the ORC, Cdc6, and Cdt1 – involving several ATP controlled recruiting events. First, the ORC and Cdc6 form a complex on origin DNA (marked by ARS type regions). New ORC/Cdc6 complexes then recruit Cdt1/Mcm2-7 molecules to the site. Once this massive ORC/Cdc6/Cdt1/Mcm2-7 (OCCM) complex is formed, the ORC/Cdc6/Cdt1 molecules work together to load Mcm2-7 onto the DNA itself by hydrolysis of ATP by Cdc6. Cdc6's phosphorylative activity is dependent on both the ORC and origin DNA. This leads to Cdt1 having decreased stability on the DNA and falling off of the complex leading to Mcm2-7 loading on to the DNA.[26][24][27][28] The structure of the ORC, MCM, as well as the intermediate OCCM complex has been resolved.[29]

CDC6 Function.jpgEukPreRC.jpg

Origin binding activity

Although the ORC is composed of six discrete subunits, only one of these has been found to be significant - ORC1. In vivo studies have shown that Lys-263 and Arg-367 are the basic residues responsible for faithful ORC loading. These molecules represent the above-mentioned ARS.[30] ORC1 interacts with ATP and these basic residues in order to bind the ORC to origin DNA. It has been established that this occurs far before replication, and that the ORC itself is already bound to Origin DNA by the time any Mcm2-7 loading occurs.[28] When Mcm2-7 is first loaded it completely encircles the DNA and helicase activity is inhibited. In S phase, the Mcm2-7 complex interacts with helicase cofactors Cdc45 and GINS to isolate a single DNA strand, unwind the origin, and begin replication down the chromosome. In order to have bidirectional replication, this process happens twice at an origin. Both loading events are mediated by one ORC via an identical process as the first.[31]

See also

References

  1. ^ Origin+Recognition+Complex at the US National Library of Medicine Medical Subject Headings (MeSH)
  2. ^ Dutta A, Bell SP (1997). "Initiation of DNA replication in eukaryotic cells". Annu. Rev. Cell Dev. Biol. 13: 293–332. doi:10.1146/annurev.cellbio.13.1.293. PMID 9442876.
  3. ^ Chesnokov IN (2007). "Multiple functions of the origin recognition complex". Int. Rev. Cytol. International Review of Cytology. 256: 69–109. doi:10.1016/S0074-7696(07)56003-1. ISBN 9780123737007. PMID 17241905.
  4. ^ a b c Matsuda K, Makise M, Sueyasu Y, Takehara M, Asano T, Mizushima T (December 2007). "Yeast two-hybrid analysis of the origin recognition complex of Saccharomyces cerevisiae: interaction between subunits and identification of binding proteins". FEMS Yeast Res. 7 (8): 1263–9. doi:10.1111/j.1567-1364.2007.00298.x. PMID 17825065.
  5. ^ a b Bell SP, Stillman B (May 1992). "ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex". Nature. 357 (6374): 128–34. doi:10.1038/357128a0. PMID 1579162.
  6. ^ a b Bell SP, Mitchell J, Leber J, Kobayashi R, Stillman B (November 1995). "The multidomain structure of Orc1p reveals similarity to regulators of DNA replication and transcriptional silencing". Cell. 83 (4): 563–8. doi:10.1016/0092-8674(95)90096-9. PMID 7585959.
  7. ^ a b c Gibson DG, Bell SP, Aparicio OM (June 2006). "Cell cycle execution point analysis of ORC function and characterization of the checkpoint response to ORC inactivation in Saccharomyces cerevisiae". Genes Cells. 11 (6): 557–73. doi:10.1111/j.1365-2443.2006.00967.x. PMID 16716188.
  8. ^ Rao H, Stillman B (March 1995). "The origin recognition complex interacts with a bipartite DNA binding site within yeast replicators". Proc. Natl. Acad. Sci. U.S.A. 92 (6): 2224–8. doi:10.1073/pnas.92.6.2224. PMC 42456. PMID 7892251.
  9. ^ Rowley A, Cocker JH, Harwood J, Diffley JF (June 1995). "Initiation complex assembly at budding yeast replication origins begins with the recognition of a bipartite sequence by limiting amounts of the initiator, ORC". EMBO J. 14 (11): 2631–41. doi:10.1002/j.1460-2075.1995.tb07261.x. PMC 398377. PMID 7781615.
  10. ^ a b Speck C, Chen Z, Li H, Stillman B (November 2005). "ATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA". Nat. Struct. Mol. Biol. 12 (11): 965–71. doi:10.1038/nsmb1002. PMC 2952294. PMID 16228006.
  11. ^ Kelly TJ, Brown GW (2000). "Regulation of chromosome replication". Annu. Rev. Biochem. 69: 829–80. doi:10.1146/annurev.biochem.69.1.829. PMID 10966477.
  12. ^ Bell SP, Dutta A (2002). "DNA replication in eukaryotic cells". Annu. Rev. Biochem. 71: 333–74. doi:10.1146/annurev.biochem.71.110601.135425. PMID 12045100.
  13. ^ Stillman B (February 2005). "Origin recognition and the chromosome cycle". FEBS Lett. 579 (4): 877–84. doi:10.1016/j.febslet.2004.12.011. PMID 15680967.
  14. ^ Weinreich M, Liang C, Chen HH, Stillman B (September 2001). "Binding of cyclin-dependent kinases to ORC and Cdc6p regulates the chromosome replication cycle". Proc. Natl. Acad. Sci. U.S.A. 98 (20): 11211–7. doi:10.1073/pnas.201387198. PMC 58709. PMID 11572976.
  15. ^ Nguyen VQ, Co C, Li JJ (June 2001). "Cyclin-dependent kinases prevent DNA re-replication through multiple mechanisms". Nature. 411 (6841): 1068–73. doi:10.1038/35082600. PMID 11429609.
  16. ^ Archambault V, Ikui AE, Drapkin BJ, Cross FR (August 2005). "Disruption of mechanisms that prevent rereplication triggers a DNA damage response". Mol. Cell. Biol. 25 (15): 6707–21. doi:10.1128/MCB.25.15.6707-6721.2005. PMC 1190345. PMID 16024805.
  17. ^ Triolo T, Sternglanz R (May 1996). "Role of interactions between the origin recognition complex and SIR1 in transcriptional silencing". Nature. 381 (6579): 251–3. doi:10.1038/381251a0. PMID 8622770.
  18. ^ Fox CA, Ehrenhofer-Murray AE, Loo S, Rine J (June 1997). "The origin recognition complex, SIR1, and the S phase requirement for silencing". Science. 276 (5318): 1547–51. doi:10.1126/science.276.5318.1547. PMID 9171055.
  19. ^ Klemm RD, Austin RJ, Bell SP (February 1997). "Coordinate binding of ATP and origin DNA regulates the ATPase activity of the origin recognition complex". Cell. 88 (4): 493–502. doi:10.1016/S0092-8674(00)81889-9. PMID 9038340.
  20. ^ Klemm RD, Bell SP (July 2001). "ATP bound to the origin recognition complex is important for preRC formation". Proc. Natl. Acad. Sci. U.S.A. 98 (15): 8361–7. doi:10.1073/pnas.131006898. PMC 37444. PMID 11459976.
  21. ^ Bowers JL, Randell JC, Chen S, Bell SP (December 2004). "ATP hydrolysis by ORC catalyzes reiterative Mcm2-7 assembly at a defined origin of replication". Mol. Cell. 16 (6): 967–78. doi:10.1016/j.molcel.2004.11.038. PMID 15610739.
  22. ^ Randell JC, Bowers JL, Rodriguez HK, Bell SP (January 2006). "Sequential ATP hydrolysis by Cdc6 and ORC directs loading of the Mcm2-7 helicase". Mol. Cell. 21 (1): 29–39. doi:10.1016/j.molcel.2005.11.023. PMID 16387651.
  23. ^ Semple JW, Da-Silva LF, Jervis EJ, Ah-Kee J, Al-Attar H, Kummer L, Heikkila JJ, Pasero P, Duncker BP (November 2006). "An essential role for Orc6 in DNA replication through maintenance of pre-replicative complexes". EMBO J. 25 (21): 5150–8. doi:10.1038/sj.emboj.7601391. PMC 1630405. PMID 17053779.
  24. ^ a b c d Morgan, David (2007). The Cell Cycle: Principles of Control. Primers in Biology. pp. 62–75. ISBN 978-0878935086.
  25. ^ Ausiannikava, Darya; Allers, Thorsten (31 January 2017). "Diversity of DNA Replication in the Archaea". Genes. 8 (2): 56. doi:10.3390/genes8020056. PMC 5333045. PMID 28146124.
  26. ^ Fernández-Cid, Alejandra (Winter 2017). "An ORC/Cdc6/MCM2-7 Complex Is Formed in a Multistep Reaction to Serve as a Platform for MCM Double-Hexamer Assembly". Molecular Cell. 50 (4): 577–588. doi:10.1016/j.molcel.2013.03.026. PMID 23603117.
  27. ^ Randell, John (Winter 2017). "Sequential ATP Hydrolysis by Cdc6 and ORC Directs Loading of the Mcm2-7 Helicase". Molecular Cell. 21: 29–39. doi:10.1016/j.molcel.2005.11.023. PMID 16387651.
  28. ^ a b Speck, Christian (Winter 2017). "ATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA". Nature Structural & Molecular Biology. 12 (11): 965–971. doi:10.1038/nsmb1002. PMC 2952294. PMID 16228006.
  29. ^ Yuan, Zuanning; Riera, Alberto; Bai, Lin; Sun, Jingchuan; Nandi, Saikat; Spanos, Christos; Chen, Zhuo Angel; Barbon, Marta; Rappsilber, Juri; Stillman, Bruce; Speck, Christian; Li, Huilin (13 February 2017). "Structural basis of Mcm2–7 replicative helicase loading by ORC–Cdc6 and Cdt1". Nature Structural & Molecular Biology. 24 (3): 316–324. doi:10.1038/nsmb.3372. PMC 5503505. PMID 28191893.
  30. ^ Kawakami, Hironori (Winter 2017). "Specific binding of eukaryotic ORC to DNA replication origins depends on highly conserved basic residues". Scientific Reports. 5: 14929. doi:10.1038/srep14929. PMC 4601075. PMID 26456755.
  31. ^ Chistol, Gheorghe (Winter 2017). "Single-Molecule Visualization of MCM2-7 DNA Loading: Seeing Is Believing". Cell. 161 (3): 429–430. doi:10.1016/j.cell.2015.04.006. PMID 25910200.

Further reading

This article incorporates text from the public domain Pfam and InterPro: IPR007220
This article incorporates text from the public domain Pfam and InterPro: IPR010748
This article incorporates text from the public domain Pfam and InterPro: IPR008721

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.

Origin recognition complex (ORC) subunit 4 C-terminus Provide feedback

This entry represents the C-terminus of origin recognition complex subunit 4 [1,2].

Literature references

  1. Quintana DG, Hou Zh, Thome KC, Hendricks M, Saha P, Dutta A;, J Biol Chem. 1997;272:28247-28251.: Identification of HsORC4, a member of the human origin of replication recognition complex. PUBMED:9353276 EPMC:9353276

  2. Chuang RY, Kelly TJ;, Proc Natl Acad Sci U S A. 1999;96:2656-2661.: The fission yeast homologue of Orc4p binds to replication origin DNA via multiple AT-hooks. PUBMED:10077566 EPMC:10077566

This tab holds annotation information from the InterPro database.

InterPro entry IPR032705

This entry represents the C terminus of origin recognition complex subunit 4 [PUBMED:9353276, PUBMED:10077566].

The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 [PUBMED:17241905]. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle [PUBMED:17825065]. ORC directs DNA replication throughout the genome and is required for its initiation [PUBMED:1579162, PUBMED:7585959, PUBMED:16716188]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [PUBMED:7892251, PUBMED:7781615, PUBMED:16228006]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [PUBMED:10966477, PUBMED:12045100, PUBMED:15680967]. Cell cycle-regulated phosphorylation of ORC2, ORC6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [PUBMED:17825065, PUBMED:11572976, PUBMED:11429609, PUBMED:16024805].

In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [PUBMED:1579162, PUBMED:7585959, PUBMED:16716188]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [PUBMED:16716188, PUBMED:8622770, PUBMED:9171055].

Both ORC1 and ORC5 bind ATP, although only ORC1 has ATPase activity [PUBMED:9038340]. The binding of ATP by ORC1 is required for ORC binding to DNA and is essential for cell viability [PUBMED:16228006]. The ATPase activity of ORC1 is involved in formation of the pre-RC [PUBMED:11459976, PUBMED:15610739, PUBMED:16387651]. ATP binding by ORC5 is crucial for the stability of ORC as a whole. Only the ORC1-5 subunits are required for origin binding; ORC6 is essential for maintenance of pre-RCs once formed [PUBMED:17053779]. Interactions within ORC suggest that ORC2-3-6 may form a core complex [PUBMED:17825065].

ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans [PUBMED:9442876].

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 AAA_lid (CL0671), which has the following description:

Many AAA+ proteins have a C-terminal alpha-helical bundle in addition to the AAA core [1]. The functional roles of the helical bundle are varied and include the formation of a lid over the nucleotide binding site and mediation of subunit interactions in oligomeric protein complexes [1].

The clan contains the following 22 members:

AAA_assoc_2 AAA_lid_1 AAA_lid_10 AAA_lid_11 AAA_lid_2 AAA_lid_3 AAA_lid_4 AAA_lid_5 AAA_lid_6 AAA_lid_7 AAA_lid_8 AAA_lid_9 CbbQ_C ClpB_D2-small Dpoe2NT MCM_lid Mg_chelatase_C ORC4_C PCP_red TIP49_C UVR Vps4_C

Alignments

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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(135)		 Full
(1223)		 Representative proteomes UniProt
(1970)		 NCBI
(2567)		 Meta
(1)
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(207)		 RP35
(544)		 RP55
(892)		 RP75
(1261)
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  Seed
(135)		 Full
(1223)		 Representative proteomes UniProt
(1970)		 NCBI
(2567)		 Meta
(1)
RP15
(207)		 RP35
(544)		 RP55
(892)		 RP75
(1261)
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  Seed
(135)		 Full
(1223)		 Representative proteomes UniProt
(1970)		 NCBI
(2567)		 Meta
(1)
RP15
(207)		 RP35
(544)		 RP55
(892)		 RP75
(1261)
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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

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.

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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 View help on the curation process

Seed source: Jackhmmer:O43929
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Eberhardt R
Number in seed: 135
Number in full: 1223
Average length of the domain: 201.70 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 35.46 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.3 25.3
Trusted cut-off 26.1 25.3
Noise cut-off 25.2 25.2
Model length: 221
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this domain across different species. More...

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Structures

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 ORC4_C domain has been found. There are 7 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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