SMC protein explained

SMC complexes represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics.^{[1] [2] [3]} SMC stands for Structural Maintenance of Chromosomes.

Classification

Eukaryotic SMCs

Eukaryotes have at least six SMC proteins in individual organisms, and they form three distinct heterodimers with specialized functions:

• A pair of SMC1 and SMC3 constitutes the core subunits of the cohesin complexes involved in sister chromatid cohesion.^{[4] [5] [6]} SMC1 and SMC3 also have functions in the repair of DNA double-strained breaks in the process of homologous recombination.^[7]
• Likewise, a pair of SMC2 and SMC4 acts as the core of the condensin complexes implicated in chromosome condensation.^{[8] [9]} SMC2 and SMC4 have the function of DNA repair as well. Condensin I plays a role in single-strained break repair but not in double-strained breaks. The opposite is true for Condensin II, which plays a role in homologous recombination.
• A dimer composed of SMC5 and SMC6 functions as part of a yet-to-be-named complex implicated in DNA repair and checkpoint responses.^[10]

Each complex contains a distinct set of non-SMC regulatory subunits. Some organisms have variants of SMC proteins. For instance, mammals have a meiosis-specific variant of SMC1, known as SMC1β.^[11] The nematode Caenorhabditis elegans has an SMC4-variant that has a specialized role in dosage compensation.^[12]

The following table shows the SMC proteins names for several model organisms and vertebrates:^[13]

Subfamily	Complex					Vertebrates
SMC1α		Smc1	Psm1	SMC-1	DmSmc1	SMC1α
SMC2		Smc2	Cut14	MIX-1	DmSmc2	CAP-E/SMC2
SMC3		Smc3	Psm3	SMC-3	DmSmc3	SMC3
SMC4		Smc4	Cut3	SMC-4	DmSmc4	CAP-C/SMC4
SMC5	SMC5-6	Smc5	Smc5	C27A2.1	CG32438	SMC5
SMC6	SMC5-6	Smc6	Smc6/Rad18	C23H4.6, F54D5.14	CG5524	SMC6
SMC1β	Cohesin (meiotic)	-	-	-	-	SMC1β
SMC4 variant	Dosage compensation complex	-	-	DPY-27	-	-

Prokaryotic SMCs

SMC proteins are conserved from bacteria to humans.^{[14] [15]} Most bacteria have a single SMC protein in individual species that forms a homodimer.^{[16] [17]} Recently SMC proteins have been shown to aid the daughter cells DNA at the origin of replication to guarantee proper segregation. In a subclass of Gram-negative bacteria, including Escherichia coli, a distantly related protein known as MukB plays an equivalent role.^[18]

Molecular structure

Primary structure

SMC proteins are 1,000-1,500 amino-acid long. They have a modular structure that is composed of the following domains:

1. Walker A ATP-binding motif
2. coiled-coil region I
3. hinge region
4. coiled-coil region II
5. Walker B ATP-binding motif; signature motif

Secondary and tertiary structure

SMC dimers form a V-shaped molecule with two long coiled-coil arms.^{[19] [20]} To make such a unique structure, an SMC protomer is self-folded through anti-parallel coiled-coil interactions, forming a rod-shaped molecule. At one end of the molecule, the N-terminal and C-terminal domains form an ATP-binding domain. The other end is called a hinge domain. Two protomers then dimerize through their hinge domains and assemble a V-shaped dimer.^{[21] [22]} The length of the coiled-coil arms is ~50 nm long. Such long "antiparallel" coiled coils are very rare and found only among SMC proteins (and their relatives such as Rad50). The ATP-binding domain of SMC proteins is structurally related to that of ABC transporters, a large family of transmembrane proteins that actively transport small molecules across cellular membranes. It is thought that the cycle of ATP binding and hydrolysis modulates the cycle of closing and opening of the V-shaped molecule. Still, the detailed mechanisms of action of SMC proteins remain to be determined.

Aggregation of SMC

The SMC proteins have the potential to form a larger ring-like structure. The ability to create different architectural arrangements allows for various regulations of functions. Some of the possible configurations are double rings, filaments, and rosettes. Double rings are 4 SMC proteins bound at the heads and hinge, forming a ring. Filaments are a chain of alternating SMCs. Rosettes are rose-like structures with terminal segments in the inner region and hinge in the outer region.^[23]

Genes

The following human genes encode SMC proteins:

• SMC1A
• SMC1B
• SMC2
• SMC3
• SMC4
• SMC5
• SMC6

See also

• cohesin
• condensin
• Cornelia de Lange Syndrome

Notes and References

1. Losada A, Hirano T . Dynamic molecular linkers of the genome: the first decade of SMC proteins . Genes Dev . 19 . 11 . 1269–1287 . 2005. 10.1101/gad.1320505 . 15937217. free .
2. Nasmyth K, Haering CH . The structure and function of SMC and kleisin complexes.. Annu. Rev. Biochem. . 74 . 595–648. 2005 . 15952899 . 10.1146/annurev.biochem.74.082803.133219.
3. Huang CE, Milutinovich M, Koshland D . Rings, bracelet or snaps: fashionable alternatives for Smc complexes. Philos Trans R Soc Lond B Biol Sci . 360 . 1455 . 537–42 . 2005. 10.1098/rstb.2004.1609 . 15897179 . 1569475.
4. Michaelis C, Ciosk R, Nasmyth K . Cohesins: chromosomal proteins that prevent premature separation of sister chromatids . Cell. 91 . 1 . 35–45. 1997 . 9335333 . 10.1016/S0092-8674(01)80007-6. free .
5. Guacci V, Koshland D, Strunnikov A . A direct link between sister chromatid cohesion and chromosome condensation revealed through the analysis of MCD1 in S. cerevisiae . Cell . 91 . 1 . 47–57. 1998 . 9335334 . 2670185 . 10.1016/S0092-8674(01)80008-8.
6. Losada A, Hirano M, Hirano T . Identification of Xenopus SMC protein complexes required for sister chromatid cohesion . Genes Dev. . 12 . 13 . 1986–1997. 1998 . 9649503 . 316973 . 10.1101/gad.12.13.1986.
7. Wu N, Yu H . The Smc complexes in DNA damage response . Cell & Bioscience . 2 . 1 . 5 . February 2012 . 22369641 . 3329402 . 10.1186/2045-3701-2-5 . free .
8. Hirano T, Kobayashi R, Hirano M . Condensins, chromosome condensation complex containing XCAP-C, XCAP-E and a Xenopus homolog of the Drosophila Barren protein . Cell . 89 . 4 . 511–21 . 1997 . 9160743 . 10.1016/S0092-8674(00)80233-0. free .
9. Ono T, Losada A, Hirano M, Myers MP, Neuwald AF, Hirano T . Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells . Cell. 115 . 1 . 109–21 . 2003 . 14532007 . 10.1016/S0092-8674(03)00724-4. free .
10. Fousteri MI, Lehmann AR . A novel SMC protein complex in Schizosaccharomyces pombe contains the Rad18 DNA repair protein . EMBO J. . 19 . 7 . 1691–1702 . 2000 . 10747036 . 310237 . 10.1093/emboj/19.7.1691.
11. Revenkova E, Eijpe M, Heyting C, Gross B, Jessberger R . Novel meiosis-specific isoform of mammalian SMC1 . Mol. Cell. Biol. . 21 . 20 . 6984–6998. 2001 . 11564881 . 10.1128/MCB.21.20.6984-6998.2001 . 99874.
12. Chuang PT, Albertson DG, Meyer BJ . DPY-27:a chromosome condensation protein homolog that regulates C. elegans dosage compensation through association with the X chromosome . Cell . 79 . 3 . 459–474. 1994 . 7954812 . 10.1016/0092-8674(94)90255-0. 28228489 .
13. Schleiffer . Alexander . Kaitna . Susanne . Maurer-Stroh . Sebastian . Glotzer . Michael . Nasmyth . Kim . Eisenhaber . Frank . March 2003 . Kleisins: A Superfamily of Bacterial and Eukaryotic SMC Protein Partners . Molecular Cell . 11 . 3 . 571–575 . 10.1016/s1097-2765(03)00108-4 . 12667442 . 1097-2765. free .
14. Harvey . Susan H. . Krien . Michael J. E. . O'Connell . Matthew J. . 2002 . Structural maintenance of chromosomes (SMC) proteins, a family of conserved ATPases . Genome Biology . 3 . 2 . REVIEWS3003 . 10.1186/gb-2002-3-2-reviews3003 . 1474-760X . 11864377. 139016 . free .
15. Palecek . Jan J. . Gruber . Stephan . December 1, 2015 . Kite Proteins: a Superfamily of SMC/Kleisin Partners Conserved Across Bacteria, Archaea, and Eukaryotes . Structure . 23 . 12 . 2183–2190 . 10.1016/j.str.2015.10.004 . 1878-4186 . 26585514. free .
16. Britton RA, Lin DC, Grossman AD . Characterization of a prokaryotic SMC protein involved in chromosome partitioning. Genes Dev.. 12 . 9 . 1254–1259. 1998 . 9573042 . 316777. 10.1101/gad.12.9.1254.
17. Hirano . Tatsuya . February 15, 2002 . The ABCs of SMC proteins: two-armed ATPases for chromosome condensation, cohesion, and repair . Genes & Development . 16 . 4 . 399–414 . 10.1101/gad.955102 . 0890-9369 . 11850403. 45664625 . free .
18. Niki H, Jaffé A, Imamura R, Ogura T, Hiraga S . The new gene mukB codes for a 177 kd protein with coiled-coil domains involved in chromosome partitioning of E. coli. EMBO J.. 10 . 1 . 183–193. 1991 . 1989883. 452628. 10.1002/j.1460-2075.1991.tb07935.x.
19. Melby TE, Ciampaglio CN, Briscoe G, Erickson HP . The symmetrical structure of structural maintenance of chromosomes (SMC) and MukB proteins: long, antiparallel coiled coils, folded at a flexible hinge. J. Cell Biol.. 142 . 6 . 1595–1604 . 1998 . 9744887 . 2141774. 10.1083/jcb.142.6.1595.
20. Anderson DE, Losada A, Erickson HP, Hirano T . Condensin and cohesin display different arm conformations with characteristic hinge angles. J. Cell Biol.. 156 . 6 . 419–424 . 2002 . 11815634 . 2173330. 10.1083/jcb.200111002.
21. Haering CH, Löwe J, Hochwagen A, Nasmyth K . Molecular architecture of SMC proteins and the yeast cohesin complex.. Mol. Cell. 9 . 4 . 773–788. 2002 . 11983169 . 10.1016/S1097-2765(02)00515-4. free .
22. Hirano M, Hirano T . Hinge-mediated dimerization of SMC protein is essential for its dynamic interaction with DNA. EMBO J.. 21 . 21 . 5733–5744. 2002 . 12411491 . 131072. 10.1093/emboj/cdf575.
23. Book: Cox MM, Doudna JA, O'Donnell M . Molecular biology : principles and practice . 2015 . 978-1-4641-2614-7 . Second . New York . 905380069.