Table of contents
September 2008, Volume 15 No 9 pp889-998
About the coverEditorial
It takes time - p889
doi:10.1038/nsmb0908-889
A look at the editorial process indicates why having your paper reviewed might take some time.
Correspondence
The binding stoichiometry of CIN85 SH3 domain A and Cbl-b - pp890 - 891
Abdessamad Ababou, Mark Pfuhl & John E Ladbury
doi:10.1038/nsmb0908-890
Full Text - The binding stoichiometry of CIN85 SH3 domain A and Cbl-b | PDF (1,081 KB) - The binding stoichiometry of CIN85 SH3 domain A and Cbl-b | Supplementary information
Reply to "The binding stoichiometry of CIN85 SH3 domain A and Cbl-b" - pp891 - 892
Daniela Jozic, Nayra Cárdenes, Yonathan Lissanu Deribe, Gabriel Moncalián, Daniela Hoeller, Yvonne Groemping, Ivan Dikic, Katrin Rittinger & Jerónimo Bravo
doi:10.1038/nsmb0908-891
Full Text - Reply to "The binding stoichiometry of CIN85 SH3 domain A and Cbl-b" | PDF (993 KB) - Reply to "The binding stoichiometry of CIN85 SH3 domain A and Cbl-b"
News and Views
Insights into PPAR
from structures with endogenous and covalently bound ligands - pp893 - 895
Kendall W Nettles
doi:10.1038/nsmb0908-893
Peroxisome proliferator–activated receptor-
(PPAR) is a ligand-regulated transcription factor with crucial roles in carbohydrate and lipid metabolism and adipogenesis, but the structural details of the binding and activation by endogenous ligands are not known. Two recent studies reveal how oxidized and nitrated fatty acids uniquely bind and activate PPAR.
Full Text - Insights into PPAR from structures with endogenous and covalently bound ligands | PDF (527 KB) - Insights into PPAR from structures with endogenous and covalently bound ligands
See also: Article by Itoh et al.
How does Plasmodium falciparum stick to CSA? Let's see in the crystal - pp895 - 897
Graham A Bentley & Benoît Gamain
doi:10.1038/nsmb0908-895
The crystal structure of the CSA-binding Duffy-binding-like domain DBL3x of the VAR2CSA-encoded PfEMP1 adhesin has been solved in the free state and complexed with CSA oligosaccharides, shedding light on the major host-parasite interaction in pregnancy-associated malaria.
Full Text - How does Plasmodium falciparum stick to CSA? Let's see in the crystal | PDF (615 KB) - How does Plasmodium falciparum stick to CSA? Let's see in the crystal
See also: Article by Singh et al.
A new, leaner and meaner bacterial organelle - pp897 - 898
Sabine Heinhorst & Gordon C Cannon
doi:10.1038/nsmb0908-897
Bacteria sequester key metabolic steps into polyhedral protein compartments. A newly discovered nanocompartment reveals what it takes for its cargo protein to become encapsulated within a protein shell.
Full Text - A new, leaner and meaner bacterial organelle | PDF (183 KB) - A new, leaner and meaner bacterial organelle
See also: Article by Sutter et al.
Sister chromatids caught in the cohesin trap - pp899 - 900
Lubos Cipak, Mario Spirek & Juraj Gregan
doi:10.1038/nsmb0908-899
Cohesin is a large ring-shaped protein complex that mediates cohesion between sister chromatids. New experiments show that the sister chromatids of a minichromosome are entrapped by monomeric cohesin rings, thus excluding the possibility that sister chromatid cohesion is mediated by nontopological interactions between cohesin complexes.
Full Text - Sister chromatids caught in the cohesin trap | PDF (300 KB) - Sister chromatids caught in the cohesin trap
Research Highlights
Research highlights - p901
doi:10.1038/nsmb0908-901
Full Text - Research highlights | PDF (146 KB) - Research highlights
Articles
Primary microRNA transcripts are processed co-transcriptionally - pp902 - 909
Mariangela Morlando, Monica Ballarino, Natalia Gromak, Francesca Pagano, Irene Bozzoni & Nick J Proudfoot
doi:10.1038/nsmb.1475
MicroRNAs are processed by Drosha, and previous data had suggested that this occurred soon after transcription. Following Drosha recruitment and using nuclear run-on technology, data now indicate that miRNAs both within and outside of introns are processed co-transcriptionally and that exonucleases enter the fray to aid processing before splicing, implying that Drosha cleavage influences the maturation of the pre-mRNAs in which miRNAs reside.
Abstract - | Full Text - Primary microRNA transcripts are processed co-transcriptionally | PDF (605 KB) - Primary microRNA transcripts are processed co-transcriptionally | Supplementary information
A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation - pp910 - 915
Sean R Connell, Maya Topf, Yan Qin, Daniel N Wilson, Thorsten Mielke, Paola Fucini, Knud H Nierhaus & Christian M T Spahn
doi:10.1038/nsmb.1469
PDB code
3D view
The ribosomal GTPase, LepA or EF4, can promote back-translocation of tRNAs, thus reversing translocation. The cryo-EM structure of the ribosome with EF4 now suggests how such back-translocation can be allowed to occur and reveals that the tRNA is in an intermediate state that deviates from its canonical position.
Abstract - | Full Text - A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation | PDF (786 KB) - A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation | Supplementary information
SRP RNA controls a conformational switch regulating the SRP–SRP receptor interaction - pp916 - 923
Saskia B Neher, Niels Bradshaw, Stephen N Floor, John D Gross & Peter Walter
doi:10.1038/nsmb.1467
The interaction between the signal-recognition particle (SRP) and its receptor (SR) is catalyzed by the RNA component of SRP, but the mechanism is not clear. Now, kinetics and NMR studies reveal an inhibitory role of the N-terminal helices of both proteins, suggesting that the RNA facilitates formation of the SRP–SR complex by promoting conformational changes of these helices.
Abstract - | Full Text - SRP RNA controls a conformational switch regulating the SRP–SRP receptor interaction | PDF (861 KB) - SRP RNA controls a conformational switch regulating the SRP–SRP receptor interaction | Supplementary information
Structural basis for the activation of PPAR by oxidized fatty acids - pp924 - 931
Toshimasa Itoh, Louise Fairall, Kush Amin, Yuka Inaba, Attila Szanto, Balint L Balint, Laszlo Nagy, Keiko Yamamoto & John W R Schwabe
doi:10.1038/nsmb.1474
PPAR is a nuclear receptor that regulates metabolic homeostasis and whose physiological ligands are nitrated and oxidized fatty acids. The crystal structures of the ligand binding domain of PPAR in complex with several oxidized fatty acids are now described, showing differences with synthetic agonists that may have physiological relevance.
Abstract - | Full Text - Structural basis for the activation of PPAR by oxidized fatty acids | PDF (1,022 KB) - Structural basis for the activation of PPAR by oxidized fatty acids | Supplementary information
See also: News and Views by Nettles
Structure of the DBL3x domain of pregnancy-associated malaria protein VAR2CSA complexed with chondroitin sulfate A - pp932 - 938
Kavita Singh, Apostolos G Gittis, Phuc Nguyen, D Channe Gowda, Louis H Miller & David N Garboczi
doi:10.1038/nsmb.1479
In pregnancy-associated malaria, parasite-infected erythrocytes express the protein VAR2CSA on their surface and bind to chondroitin sulfate A in the placenta, with severe effects to the mother and the fetus. Now the crystal structure of a domain of VAR2CSA in complex with chondroitin sulfate A is reported and, together with functional studies, sheds insight into this interaction.
Abstract - | Full Text - Structure of the DBL3x domain of pregnancy-associated malaria protein VAR2CSA complexed with chondroitin sulfate A | PDF (645 KB) - Structure of the DBL3x domain of pregnancy-associated malaria protein VAR2CSA complexed with chondroitin sulfate A | Supplementary information
See also: News and Views by Bentley & Gamain
Structural basis of enzyme encapsulation into a bacterial nanocompartment - pp939 - 947
Markus Sutter, Daniel Boehringer, Sascha Gutmann, Susanne Günther, David Prangishvili, Martin J Loessner, Karl O Stetter, Eilika Weber-Ban & Nenad Ban
doi:10.1038/nsmb.1473
PDB code
3D view
Certain bacterial enzymes are packaged within protein chambers that provide a confined environment for their reactions to take place. Ban and colleagues now identify a family of proteins that form nanocompartments, similar to bacterial microcompartments such as the carboxysome, and show that the enzymes within are anchored by their C-terminal extensions to binding sites on the inner surface of the chamber.
Abstract - | Full Text - Structural basis of enzyme encapsulation into a bacterial nanocompartment | PDF (972 KB) - Structural basis of enzyme encapsulation into a bacterial nanocompartment | Supplementary information
See also: News and Views by Heinhorst & Cannon
Molecular functions of the histone acetyltransferase chaperone complex Rtt109–Vps75 - pp948 - 956
Christopher E Berndsen, Toshiaki Tsubota, Scott E Lindner, Susan Lee, James M Holton, Paul D Kaufman, James L Keck & John M Denu
doi:10.1038/nsmb.1459
Vps75 is a histone chaperone that associates with the Rtt109 acteyltransferase. The structure of Vps75 and further biochemical analysis suggest how Vps75 functions to alter histone H3K9 acetylation during S phase, and suggest a model for how it activates the histone acetyltransferase.
Abstract - | Full Text - Molecular functions of the histone acetyltransferase chaperone complex Rtt109–Vps75 | PDF (789 KB) - Molecular functions of the histone acetyltransferase chaperone complex Rtt109–Vps75 | Supplementary information
Histone chaperone specificity in Rtt109 activation - pp957 - 964
Young-Jun Park, Keely B Sudhoff, Andrew J Andrews, Laurie A Stargell & Karolin Luger
doi:10.1038/nsmb.1480
PDB code
3D view
The structure of yeast Vps75, a histone chaperone that associates with the Rtt109 histone acetyltransferase, is presented and compared to Nap1, which interacts with the same histone acetyltransferase.
Abstract - | Full Text - Histone chaperone specificity in Rtt109 activation | PDF (691 KB) - Histone chaperone specificity in Rtt109 activation | Supplementary information
A regulatable switch mediates self-association in an immunoglobulin fold - pp965 - 971
Matthew F Calabrese, Catherine M Eakin, Jimin M Wang & Andrew D Miranker
doi:10.1038/nsmb.1483
PDB code
3D view
Formation of 
-2 microglobulin (2m) amyloid fibrils is associated with dialysis-related amyloidosis. 2m pre-amyloid formation occurs in a Cu2+-dependent manner in vitro. Structural studies reveal that structural changes away from the Cu2+ binding site create conditions that promote 2m oligomerization leading to amyloidogenesis.
Abstract - | Full Text - A regulatable switch mediates self-association in an immunoglobulin fold | PDF (1,223 KB) - A regulatable switch mediates self-association in an immunoglobulin fold | Supplementary information
The HP1–p150/CAF-1 interaction is required for pericentric heterochromatin replication and S-phase progression in mouse cells - pp972 - 979
Jean-Pierre Quivy, Annabelle Gérard, Adam J L Cook, Danièle Roche & Geneviève Almouzni
doi:10.1038/nsmb.1470
The architecture of heterochromatin is maintained by HP1, which is known to interact with the p150 subunit from the histone chaperone complex CAF-1. This interaction is now shown to be important for the replication of pericentric heterochromatin regions during late S phase in mouse cells, a role that is independent of CAF-1's histone-deposition activity.
Abstract - | Full Text - The HP1–p150/CAF-1 interaction is required for pericentric heterochromatin replication and S-phase progression in mouse cells | PDF (685 KB) - The HP1–p150/CAF-1 interaction is required for pericentric heterochromatin replication and S-phase progression in mouse cells | Supplementary information
Structural basis for group A trichothiodystrophy - pp980 - 984
Denis E Kainov, Marc Vitorino, Jean Cavarelli, Arnaud Poterszman & Jean-Marc Egly
doi:10.1038/nsmb.1478
Group A trichothiodystrophy is caused by mutations in the p8 subunit of the TFIIH complex, involved in transcription and nucleotide-excision repair. Now the structure of the yeast ortholog of p8 in complex with a fragment of the yeast ortholog of p52 shows how p8 stabilizes p52 and thus the whole TFIIH complex.
Abstract - | Full Text - Structural basis for group A trichothiodystrophy | PDF (569 KB) - Structural basis for group A trichothiodystrophy | Supplementary information
A proposed OB-fold with a protein-interaction surface in Candida albicans telomerase protein Est3 - pp985 - 989
Eun Young Yu, Feng Wang, Ming Lei & Neal F Lue
doi:10.1038/nsmb.1471
The Est3 telomerase subunit has a critical, but still uncharacterized regulatory role in yeast telomere maintenance. An OB-fold is now predicted for Candida albicans Est3 protein, and residues important for its association with the telomerase complex are identified.
Abstract - | Full Text - A proposed OB-fold with a protein-interaction surface in Candida albicans telomerase protein Est3 | PDF (722 KB) - A proposed OB-fold with a protein-interaction surface in Candida albicans telomerase protein Est3 | Supplementary information
The Est3 protein associates with yeast telomerase through an OB-fold domain - pp990 - 997
Jaesung Lee, Edward K Mandell, Timothy M Tucey, Danna K Morris & Victoria Lundblad
doi:10.1038/nsmb.1472
The Est3 telomerase subunit has a critical, but still uncharacterized regulatory role in yeast telomere maintenance. An OB-fold is now predicted for Saccharomyces cerevisiae Est3 protein, and residues important for its association with the telomerase complex are identified.
Abstract - | Full Text - The Est3 protein associates with yeast telomerase through an OB-fold domain | PDF (984 KB) - The Est3 protein associates with yeast telomerase through an OB-fold domain | Supplementary information
Corrigenda
Single-molecule studies of fork dynamics in Escherichia coli DNA replication - p998
Nathan A Tanner, Samir M Hamdan, Slobodan Jergic, Karin V Loscha, Patrick M Schaeffer, Nicholas E Dixon & Antoine M van Oijen
doi:10.1038/nsmb0908-998a
Full Text - Single-molecule studies of fork dynamics in Escherichia coli DNA replication | PDF (92 KB) - Single-molecule studies of fork dynamics in Escherichia coli DNA replication
A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases - p998
Roberta Benetti, Susana Gonzalo, Isabel Jaco, Purificación Muñoz, Susana Gonzalez, Stefan Schoeftner, Elizabeth Murchison, Thomas Andl, Taiping Chen, Peter Klatt, En Li, Manuel Serrano, Sarah Millar, Gregory Hannon & Maria A Blasco
doi:10.1038/nsmb0908-998b
Full Text - A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases | PDF (92 KB) - A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases
Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster - p998
Katsutomo Okamura, Sudha Balla, Raquel Martin, Na Liu & Eric C Lai
doi:10.1038/nsmb0908-998c
Full Text - Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster | PDF (92 KB) - Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster
Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP - p998
Yong Tang, Marc A Holbert, Hugo Wurtele, Katrina Meeth, Walter Rocha, Marlene Gharib, Eva Jiang, Pierre Thibault, Alain Verreault, Philip A Cole & Ronen Marmorstein
doi:10.1038/nsmb0908-998d
Full Text - Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP | PDF (92 KB) - Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP
