Structural Basis for a Safety-Belt Mechanism That Anchors Condensin to Chromosomes

Abstract

SummaryCondensin protein complexes coordinate the formation of mitotic chromosomes and thereby ensure the successful segregation of replicated genomes. Insights into how condensin complexes bind to chromosomes and alter their topology are essential for understanding the molecular principles behind the large-scale chromatin rearrangements that take place during cell divisions. Here, we identify a direct DNA-binding site in the eukaryotic condensin complex, which is formed by its Ycg1Cnd3 HEAT-repeat and Brn1Cnd2 kleisin subunits. DNA co-crystal structures reveal a conserved, positively charged groove that accommodates the DNA double helix. A peptide loop of the kleisin subunit encircles the bound DNA and, like a safety belt, prevents its dissociation. Firm closure of the kleisin loop around DNA is essential for the association of condensin complexes with chromosomes and their DNA-stimulated ATPase activity. Our data suggest a sophisticated molecular basis for anchoring condensin complexes to chromosomes that enables the formation of large-sized chromatin loops.

Structural basis ofHEAT‐kleisin interactions in the human condensin I subcomplex

“…The colored circles indicate residues of hCAP‐H that interact with hCAP‐G (orange) and residues of BRN1 that interact with YCG1 (purple) or dsDNA (red). BC1, BC2, latch, and buckle regions defined by Kschonsak et al , and motifs III and IV of CAP‐H are also shown in Fig A.…”

“…Residues of YCG1 that interact with BRN1 and dsDNA are labeled with light blue and red, respectively. The YC1 and YC2 regions indicate residues essential for DNA binding defined by Kschonsak et al . Structure‐based sequence alignment of hCAP‐H, XCAP‐H, and BRN1. The secondary structural elements of hCAP‐H and BRN1 are drawn above and below the sequence alignments, respectively.…”

Real‐time detection of condensin‐driven DNA compaction reveals a multistep binding mechanism

“…To specifically test the requirement for the Ycg1–Brn1 DNA‐binding groove, we repeated the experiment with a version of the condensin holocomplex that contains charge‐reversal mutations in the DNA‐binding groove. This mutant can still hydrolyse ATP, but its ATPase activity is not stimulated by the presence of DNA (Kschonsak et al , ). Consistent with the result for the tetrameric complex, this complex was also unable to induce DNA compaction in our assay (Fig EV3B).…”

“…If the interaction of condensin with DNA would only be topological, loop extrusion would not work, as DNA can slip out of the ring, which certainly will happen under an applied force. Our finding that a direct (electrostatic) contact between condensin and DNA is required to maintain the compacted state of DNA suggests that such a contact might serve as an anchor site at the base of a forming loop (Kschonsak et al , ). The finding that halfway compacted DNA molecules can eventually compact fully without the addition of extra protein is furthermore easy to imagine for a motor extruding a loop of ever‐larger size.…”

Structural Biology of the HEAT‐Like Repeat Family of DNA Glycosylases

“…HEAT domains are also involved in binding and transporting protein ligands within the inner channel of the superhelix . More recently, this channel has been identified as a nucleic acid binding surface in a set of proteins with diverse functions, including RNA nuclear export, regulation of mRNA stability, and chromosome segregation …”