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PDBsum entry 1e69

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protein Protein-protein interface(s) links
Chromosome segregation PDB id
1e69
Jmol
Contents
Protein chains
(+ 0 more) 263 a.a. *
* Residue conservation analysis
PDB id:
1e69
Name: Chromosome segregation
Title: Smc head domain from thermotoga maritima
Structure: Chromosome segregation smc protein. Chain: a, b, c, d, e, f. Fragment: smc fusion of the n- and c-terminal globular domains residues 1-152 and 1023-1164. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Atcc: dsm3109. Cellular_location: cytosol. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.1Å     R-factor:   0.250     R-free:   0.272
Authors: J.Lowe,S.C.Cordell,F.Van Den Ent
Key ref:
J.Löwe et al. (2001). Crystal structure of the SMC head domain: an ABC ATPase with 900 residues antiparallel coiled-coil inserted. J Mol Biol, 306, 25-35. PubMed id: 11178891 DOI: 10.1006/jmbi.2000.4379
Date:
09-Aug-00     Release date:   09-Aug-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9X0R4  (Q9X0R4_THEMA) -  Chromosome partition protein Smc
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1170 a.a.
263 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 116 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleotide binding     2 terms  

 

 
DOI no: 10.1006/jmbi.2000.4379 J Mol Biol 306:25-35 (2001)
PubMed id: 11178891  
 
 
Crystal structure of the SMC head domain: an ABC ATPase with 900 residues antiparallel coiled-coil inserted.
J.Löwe, S.C.Cordell, F.van den Ent.
 
  ABSTRACT  
 
SMC (structural maintenance of chromosomes) proteins are large coiled-coil proteins involved in chromosome condensation, sister chromatid cohesion, and DNA double-strand break processing. They share a conserved five-domain architecture with three globular domains separated by two long coiled-coil segments. The coiled-coil segments are antiparallel, bringing the N and C-terminal globular domains together. We have expressed a fusion protein of the N and C-terminal globular domains of Thermotoga maritima SMC in Escherichia coli by replacing the approximately 900 residue coiled-coil and hinge segment with a short peptide linker. The SMC head domain (SMChd) binds and condenses DNA in an ATP-dependent manner. Using selenomethionine-substituted protein and multiple anomalous dispersion phasing, we have solved the crystal structure of the SMChd to 3.1 A resolution. In the monoclinic crystal form, six SMChd molecules form two turns of a helix. The fold of SMChd is closely related to the ATP-binding cassette (ABC) ATPase family of proteins and Rad50, a member of the SMC family involved in DNA double-strand break repair. In SMChd, the ABC ATPase fold is formed by the N and C-terminal domains with the 900 residue coiled-coil and hinge segment inserted in the middle of the fold. The crystal structure of an SMChd confirms that the coiled-coil segments in SMC proteins are anti-parallel and shows how the N and C-terminal domains come together to form an ABC ATPase. Comparison to the structure of the MukB N-terminal domain demonstrates the close relationship between MukB and SMC proteins, and indicates a helix to strand conversion when N and C-terminal parts come together.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. (a) Ribbon representation of the six non-crystallographically related molecules in the asymmetric unit of the monoclinic crystal form. Six SMChd molecules form two turns of a head-to-tail 3[1] helix (prepared with MOLSCRIPT, [Kraulis 1991]). (b) Stereo representation of the six NCS-related molecules in the asymmetric unit of the trigonal space group. The same 3[1] SMChd helix as in the monoclinic crystals is formed by each of the six molecules by crystallographic P3[1] symmetry perpendicular to the paper plane (prepared with MAIN, [Turk 1992]).
Figure 5.
Figure 5. Structure-based sequence alignment of SMChd from Thermotoga maritima (PDB ID 1E69), Rad50 from Pyrococcus furiosus (PDB ID 1F2T chains A, B), the N-terminal domain of MukB from Escherichia coli (PDB ID 1QHL), and histidine permease protein HisP from Salmonella typhimurium (PDB ID 1B0U). A preliminary sequence alignment was prepared, adjusted using the DALI [Holm and Sander 1995] results and checked for all six pairs manually in three dimensions. For clarity, non-overlapping regions in three dimensions have not been separated. The numbering corresponds to SMChd, as do the secondary structural elements. The Figure was prepared with ALSCRIPT [Barton 1993].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 306, 25-35) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19906728 M.Krishnamurthy, S.Tadesse, K.Rothmaier, and P.L.Graumann (2010).
A novel SMC-like protein, SbcE (YhaN), is involved in DNA double-strand break repair and competence in Bacillus subtilis.
  Nucleic Acids Res, 38, 455-466.  
19886810 K.Nasmyth, and C.H.Haering (2009).
Cohesin: its roles and mechanisms.
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19017635 N.Makharashvili, T.Mi, O.Koroleva, and S.Korolev (2009).
RecR-mediated Modulation of RecF Dimer Specificity for Single- and Double-stranded DNA.
  J Biol Chem, 284, 1425-1434.  
18929067 P.J.Brown, G.G.Hardy, M.J.Trimble, and Y.V.Brun (2009).
Complex regulatory pathways coordinate cell-cycle progression and development in Caulobacter crescentus.
  Adv Microb Physiol, 54, 1.  
19308706 P.L.Graumann, and T.Knust (2009).
Dynamics of the bacterial SMC complex and SMC-like proteins involved in DNA repair.
  Chromosome Res, 17, 265-275.  
19748359 X.Duan, P.Sarangi, X.Liu, G.K.Rangi, X.Zhao, and H.Ye (2009).
Structural and functional insights into the roles of the Mms21 subunit of the Smc5/6 complex.
  Mol Cell, 35, 657-668.
PDB code: 3htk
18594865 H.Muraguchi, K.Abe, M.Nakagawa, K.Nakamura, and S.O.Yanagi (2008).
Identification and characterisation of structural maintenance of chromosome 1 (smc1) mutants of Coprinopsis cinerea.
  Mol Genet Genomics, 280, 223-232.  
18616427 I.Onn, J.M.Heidinger-Pauli, V.Guacci, E.Unal, and D.E.Koshland (2008).
Sister chromatid cohesion: a simple concept with a complex reality.
  Annu Rev Cell Dev Biol, 24, 105-129.  
18300244 J.S.Kim, S.Lee, B.S.Kang, M.H.Kim, H.S.Lee, and K.J.Kim (2008).
Crystal structure and domain characterization of ScpB from Mycobacterium tuberculosis.
  Proteins, 71, 1553-1556.
PDB code: 2z99
18811946 Q.Dai, and T.Wang (2008).
Comparison study on k-word statistical measures for protein: from sequence to 'sequence space'.
  BMC Bioinformatics, 9, 394.  
18283122 S.Sivasubramaniam, X.Sun, Y.R.Pan, S.Wang, and E.Y.Lee (2008).
Cep164 is a mediator protein required for the maintenance of genomic stability through modulation of MDC1, RPA, and CHK1.
  Genes Dev, 22, 587-600.  
17208306 C.A.McDevitt, and R.Callaghan (2007).
How can we best use structural information on P-glycoprotein to design inhibitors?
  Pharmacol Ther, 113, 429-441.  
17333236 P.König, M.B.Braunfeld, J.W.Sedat, and D.A.Agard (2007).
The three-dimensional structure of in vitro reconstituted Xenopus laevis chromosomes by EM tomography.
  Chromosoma, 116, 349-372.  
  18084093 S.Y.Kwon, B.S.Kang, M.H.Kim, and K.J.Kim (2007).
Cloning, expression, purification, crystallization and X-ray crystallographic analysis of ScpB (Rv1710) from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 1058-1060.  
16229890 A.V.Strunnikov (2006).
SMC complexes in bacterial chromosome condensation and segregation.
  Plasmid, 55, 135-144.  
16499625 G.Fichant, M.J.Basse, and Y.Quentin (2006).
ABCdb: an online resource for ABC transporter repertories from sequenced archaeal and bacterial genomes.
  FEMS Microbiol Lett, 256, 333-339.  
16780573 J.Mascarenhas, H.Sanchez, S.Tadesse, D.Kidane, M.Krisnamurthy, J.C.Alonso, and P.L.Graumann (2006).
Bacillus subtilis SbcC protein plays an important role in DNA inter-strand cross-link repair.
  BMC Mol Biol, 7, 20.  
16294331 J.S.Kim, D.H.Shin, R.Pufan, C.Huang, H.Yokota, R.Kim, and S.H.Kim (2006).
Crystal structure of ScpB from Chlorobium tepidum, a protein involved in chromosome partitioning.
  Proteins, 62, 322-328.
PDB code: 1t6s
16740950 Q.Wang, E.A.Mordukhova, A.L.Edwards, and V.V.Rybenkov (2006).
Chromosome condensation in the absence of the non-SMC subunits of MukBEF.
  J Bacteriol, 188, 4431-4441.  
16756491 S.K.Ghosh, S.Hajra, A.Paek, and M.Jayaram (2006).
Mechanisms for chromosome and plasmid segregation.
  Annu Rev Biochem, 75, 211-241.  
15837203 A.Karcher, K.Büttner, B.Märtens, R.P.Jansen, and K.P.Hopfner (2005).
X-ray structure of RLI, an essential twin cassette ABC ATPase involved in ribosome biogenesis and HIV capsid assembly.
  Structure, 13, 649-659.
PDB code: 1yqt
16331985 C.M.Taylor, and A.E.Keating (2005).
Orientation and oligomerization specificity of the Bcr coiled-coil oligomerization domain.
  Biochemistry, 44, 16246-16256.  
16120222 E.Larsabal, and A.Danchin (2005).
Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns".
  BMC Bioinformatics, 6, 206.  
15987505 J.Mascarenhas, A.V.Volkov, C.Rinn, J.Schiener, R.Guckenberger, and P.L.Graumann (2005).
Dynamic assembly, localization and proteolysis of the Bacillus subtilis SMC complex.
  BMC Cell Biol, 6, 28.  
15952899 K.Nasmyth, and C.H.Haering (2005).
The structure and function of SMC and kleisin complexes.
  Annu Rev Biochem, 74, 595-648.  
15797198 M.Thanbichler, P.H.Viollier, and L.Shapiro (2005).
The structure and function of the bacterial chromosome.
  Curr Opin Genet Dev, 15, 153-162.  
15902272 R.Fennell-Fezzie, S.D.Gradia, D.Akey, and J.M.Berger (2005).
The MukF subunit of Escherichia coli condensin: architecture and functional relationship to kleisins.
  EMBO J, 24, 1921-1930.
PDB code: 1t98
15897176 T.Hirano (2005).
SMC proteins and chromosome mechanics: from bacteria to humans.
  Philos Trans R Soc Lond B Biol Sci, 360, 507-514.  
15087462 A.Chiu, E.Revenkova, and R.Jessberger (2004).
DNA interaction and dimerization of eukaryotic SMC hinge domains.
  J Biol Chem, 279, 26233-26242.  
15383284 C.H.Haering, D.Schoffnegger, T.Nishino, W.Helmhart, K.Nasmyth, and J.Löwe (2004).
Structure and stability of cohesin's Smc1-kleisin interaction.
  Mol Cell, 15, 951-964.
PDB code: 1w1w
15186413 D.Kidane, H.Sanchez, J.C.Alonso, and P.L.Graumann (2004).
Visualization of DNA double-strand break repair in live bacteria reveals dynamic recruitment of Bacillus subtilis RecF, RecO and RecN proteins to distinct sites on the nucleoids.
  Mol Microbiol, 52, 1627-1639.  
15009890 E.Dervyn, M.F.Noirot-Gros, P.Mervelet, S.McGovern, S.D.Ehrlich, P.Polard, and P.Noirot (2004).
The bacterial condensin/cohesin-like protein complex acts in DNA repair and regulation of gene expression.
  Mol Microbiol, 51, 1629-1640.  
15268872 I.M.Porter, G.A.Khoudoli, and J.R.Swedlow (2004).
Chromosome condensation: DNA compaction in real time.
  Curr Biol, 14, R554-R556.  
15065662 K.Nasmyth, and A.Schleiffer (2004).
From a single double helix to paired double helices and back.
  Philos Trans R Soc Lond B Biol Sci, 359, 99.  
15196458 L.J.Wu (2004).
Structure and segregation of the bacterial nucleoid.
  Curr Opin Genet Dev, 14, 126-132.  
14701739 S.H.Harvey, D.M.Sheedy, A.R.Cuddihy, and M.J.O'Connell (2004).
Coordination of DNA damage responses via the Smc5/Smc6 complex.
  Mol Cell Biol, 24, 662-674.  
15186409 S.W.Long, and D.M.Faguy (2004).
Anucleate and titan cell phenotypes caused by insertional inactivation of the structural maintenance of chromosomes (smc) gene in the archaeon Methanococcus voltae.
  Mol Microbiol, 52, 1567-1577.  
12897137 A.Volkov, J.Mascarenhas, C.Andrei-Selmer, H.D.Ulrich, and P.L.Graumann (2003).
A prokaryotic condensin/cohesin-like complex can actively compact chromosomes from a single position on the nucleoid and binds to DNA as a ring-like structure.
  Mol Cell Biol, 23, 5638-5650.  
14635253 C.H.Haering, and K.Nasmyth (2003).
Building and breaking bridges between sister chromatids.
  Bioessays, 25, 1178-1191.  
12719426 J.E.Stray, and J.E.Lindsley (2003).
Biochemical analysis of the yeast condensin Smc2/4 complex: an ATPase that promotes knotting of circular DNA.
  J Biol Chem, 278, 26238-26248.  
12667441 J.R.Swedlow, and T.Hirano (2003).
The making of the mitotic chromosome: modern insights into classical questions.
  Mol Cell, 11, 557-569.  
14662354 K.Pogliano, J.Pogliano, and E.Becker (2003).
Chromosome segregation in Eubacteria.
  Curr Opin Microbiol, 6, 586-593.  
12554644 L.Nachin, L.Loiseau, D.Expert, and F.Barras (2003).
SufC: an unorthodox cytoplasmic ABC/ATPase required for [Fe-S] biogenesis under oxidative stress.
  EMBO J, 22, 427-437.  
12730166 R.B.Jensen, and L.Shapiro (2003).
Cell-cycle-regulated expression and subcellular localization of the Caulobacter crescentus SMC chromosome structural protein.
  J Bacteriol, 185, 3068-3075.  
12654244 S.Gruber, C.H.Haering, and K.Nasmyth (2003).
Chromosomal cohesin forms a ring.
  Cell, 112, 765-777.  
14614818 S.Weitzer, C.Lehane, and F.Uhlmann (2003).
A model for ATP hydrolysis-dependent binding of cohesin to DNA.
  Curr Biol, 13, 1930-1940.  
11983169 C.H.Haering, J.Löwe, A.Hochwagen, and K.Nasmyth (2002).
Molecular architecture of SMC proteins and the yeast cohesin complex.
  Mol Cell, 9, 773-788.
PDB codes: 1gxj 1gxk 1gxl
11815634 D.E.Anderson, A.Losada, H.P.Erickson, and T.Hirano (2002).
Condensin and cohesin display different arm conformations with characteristic hinge angles.
  J Cell Biol, 156, 419-424.  
11807278 G.Verdon, S.V.Albers, B.W.Dijkstra, A.J.Driessen, and A.M.Thunnissen (2002).
Purification, crystallization and preliminary X-ray diffraction analysis of an archaeal ABC-ATPase.
  Acta Crystallogr D Biol Crystallogr, 58, 362-365.  
12421306 J.C.Lindow, M.Kuwano, S.Moriya, and A.D.Grossman (2002).
Subcellular localization of the Bacillus subtilis structural maintenance of chromosomes (SMC) protein.
  Mol Microbiol, 46, 997.  
12218017 J.C.Lindow, R.A.Britton, and A.D.Grossman (2002).
Structural maintenance of chromosomes protein of Bacillus subtilis affects supercoiling in vivo.
  J Bacteriol, 184, 5317-5322.  
12065423 J.Mascarenhas, J.Soppa, A.V.Strunnikov, and P.L.Graumann (2002).
Cell cycle-dependent localization of two novel prokaryotic chromosome segregation and condensation proteins in Bacillus subtilis that interact with SMC protein.
  EMBO J, 21, 3108-3118.  
11752311 L.Lo Conte, S.E.Brenner, T.J.Hubbard, C.Chothia, and A.G.Murzin (2002).
SCOP database in 2002: refinements accommodate structural genomics.
  Nucleic Acids Res, 30, 264-267.  
12176928 M.Beasley, H.Xu, W.Warren, and M.McKay (2002).
Conserved disruptions in the predicted coiled-coil domains of eukaryotic SMC complexes: implications for structure and function.
  Genome Res, 12, 1201-1209.  
12411491 M.Hirano, and T.Hirano (2002).
Hinge-mediated dimerization of SMC protein is essential for its dynamic interaction with DNA.
  EMBO J, 21, 5733-5744.  
12360193 R.Jessberger (2002).
The many functions of SMC proteins in chromosome dynamics.
  Nat Rev Mol Cell Biol, 3, 767-778.  
  11864377 S.H.Harvey, M.J.Krien, and M.J.O'Connell (2002).
Structural maintenance of chromosomes (SMC) proteins, a family of conserved ATPases.
  Genome Biol, 3, REVIEWS3003.  
11378401 F.Uhlmann (2001).
Chromosome condensation: packaging the genome.
  Curr Biol, 11, R384-R387.  
11698193 F.Uhlmann (2001).
Chromosome cohesion and segregation in mitosis and meiosis.
  Curr Opin Cell Biol, 13, 754-761.  
11700297 K.Nasmyth (2001).
Disseminating the genome: joining, resolving, and separating sister chromatids during mitosis and meiosis.
  Annu Rev Genet, 35, 673-745.  
11406600 M.Hirano, D.E.Anderson, H.P.Erickson, and T.Hirano (2001).
Bimodal activation of SMC ATPase by intra- and inter-molecular interactions.
  EMBO J, 20, 3238-3250.  
11741547 M.de Jager, J.van Noort, D.C.van Gent, C.Dekker, R.Kanaar, and C.Wyman (2001).
Human Rad50/Mre11 is a flexible complex that can tether DNA ends.
  Mol Cell, 8, 1129-1135.  
11532960 R.Gaudet, and D.C.Wiley (2001).
Structure of the ABC ATPase domain of human TAP1, the transporter associated with antigen processing.
  EMBO J, 20, 4964-4972.
PDB code: 1jj7
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.