Solution NMR structures of homeodomains from human proteins ALX4, ZHX1, and CASP8AP2 contribute to the structural coverage of the Human Cancer Protein Interaction Network

citation_journal_title=J Mol Biol; citation_title=SCOP: a structural classification of proteins database for the investigation of sequences and structures; citation_author=AG Murzin, SE Brenner, T Hubbard, C Chothia; citation_volume=247; citation_publication_date=1995; citation_pages=536-540; citation_id=CR1 citation_journal_title=Nucleic Acids Res; citation_title=The Pfam protein families database; citation_author=RD Finn, J Mistry, J Tate, P Coggill, A Heger, JE Pollington, OL Gavin, P Gunasekaran, G Ceric, K Forslund, L Holm, ELL Sonnhammer, SR Eddy, A Bateman; citation_volume=38; citation_publication_date=2010; citation_pages=D211-D222; citation_doi=10.1093/nar/gkp985; citation_id=CR2 citation_journal_title=Genes Dev; citation_title=Cooperative dimerization of paired class homeo domains on DNA; citation_author=D Wilson, G Sheng, T Lecuit, N Dostatni, C Desplan; citation_volume=7; citation_publication_date=1993; citation_pages=2120-2134; citation_doi=10.1101/gad.7.11.2120; citation_id=CR3 citation_journal_title=Development; citation_title=Physical and genetic interactions between Alx4 and Cart1; citation_author=S Qu, SC Tucker, Q Zhao, B deCrombrugghe, R Wisdom; citation_volume=126; citation_publication_date=1999; citation_pages=359-369; citation_id=CR4 citation_journal_title=J Med Genet; citation_title=The ALX4 homeobox gene is mutated in patients with ossification defects of the skull (foramina parietalia permagna, OMIM 1685000); citation_author=W Wuyts, E Cleiren, T Homfray, A Rasore-Quartino, F Vanhoenacker, HW Van; citation_volume=37; citation_publication_date=2000; citation_pages=916-920; citation_doi=10.1136/jmg.37.12.916; citation_id=CR5 citation_journal_title=Hum Mol Genet; citation_title=ALX4 dysfunction disrupts craniofacial and epidermal development; citation_author=H Kayserili, E Uz, C Niessen, I Vargel, Y Alanay, G Tuncbilek, G Yigit, O Uyguner, S Candan, H Okur, S Kaygin, S Balci, E Mavili, M Alikasifoglu, I Haase, B Wollnik, NA Akarsu; citation_volume=18; citation_publication_date=2009; citation_pages=4357-4366; citation_doi=10.1093/hmg/ddp391; citation_id=CR6 citation_journal_title=Dev Biol; citation_title=Loss of Alx4, a stromally-restricted homeodomain protein, impairs mammary epithelial morphogenesis; citation_author=PA Joshi, H Chang, PA Hamel; citation_volume=297; citation_publication_date=2006; citation_pages=284-294; citation_doi=10.1016/j.ydbio.2006.05.032; citation_id=CR7 citation_journal_title=Nature Genet; citation_title=Haploinsufficiency of the human homeobox gene ALX4 causes skull ossification defects; citation_author=LA Mavrogiannis, I Antonopoulou, A Baxova, S Kutilek, CA Kim, SM Sugayama, A Salamanca, SA Wall, GM Morriss-Kay, AOM Wilkie; citation_volume=27; citation_publication_date=2001; citation_pages=17-18; citation_doi=10.1038/83703; citation_id=CR8 Liu WB, Han F, Du XH, Jiang X, Li YH, Liu Y, Chen HQ, Ao L, Cui ZH, Cao J, Liu JY (2013) Epigenetic silencing of Aristaless-like homeobox-4, a potential tumor suppressor gene associated with lung cancer. Int J Cancer 134:1311–1322 citation_journal_title=Clin Cancer Res; citation_title=A novel set of DNA methylation markers in urine sediments for sensitive/specific detection of bladder cancer; citation_author=J Yu, T Zhu, Z Wang, H Zhang, Z Qian, H Xu, B Gao, W Wang, L Gu, J Meng, J Wang, X Feng, Y Li, X Yao, J Zhu; citation_volume=13; citation_publication_date=2007; citation_pages=7296-7304; citation_doi=10.1158/1078-0432.CCR-07-0861; citation_id=CR10 citation_journal_title=Cancer Sci; citation_title=High CpG island methylator phenotype is associated with lymph node metastasis and prognosis in gastric cancer; citation_author=HY Chen, BH Zhu, CH Zhang, DJ Yang, JJ Peng, JH Chen, FK Liu, YL He; citation_volume=103; citation_publication_date=2012; citation_pages=73-79; citation_doi=10.1111/j.1349-7006.2011.02129.x; citation_id=CR11 citation_journal_title=Gastroenterology; citation_title=Aristaless-like homeobox-4 gene methylation is a potential marker for colorectal adenocarcinomas; citation_author=MP Ebert, F Model, S Mooney, K Hale, J Lograsso, L Tonnes-Priddy, J Hoffmann, A Csepregi, C Rocken, B Molnar, HU Schulz, P Malfertheiner, C Lofton-Day; citation_volume=131; citation_publication_date=2006; citation_pages=1418-1430; citation_doi=10.1053/j.gastro.2006.08.034; citation_id=CR12 citation_journal_title=PLoS ONE; citation_title=Performance of epigenetic markers SEPT9 and ALX4 in plasma for detection of colorectal precancerous lesions; citation_author=M Tanzer, B Balluff, J Distler, K Hale, A Leodolter, C Rocken, B Molnar, R Schmid, C Lofton-Day, T Schuster, MP Ebert; citation_volume=5; citation_publication_date=2010; citation_pages=e9061; citation_doi=10.1371/journal.pone.0009061; citation_id=CR13 citation_journal_title=Cancer Epidemiol Biomark Prev; citation_title=Highly methylated genes in colorectal neoplasia: implications for screening; citation_author=H Zou, JJ Harrington, AM Shire, RL Rego, L Wang, ME Campbell, AL Oberg, DA Ahlquist; citation_volume=16; citation_publication_date=2007; citation_pages=2686-2696; citation_doi=10.1158/1055-9965.EPI-07-0518; citation_id=CR14 citation_journal_title=J Clin Pathol; citation_title=Loss of ALX4 expression in epithelial cells and adjacent stromal cells in breast cancer; citation_author=H Chang, N Mohabir, S Done, PA Hamel; citation_volume=62; citation_publication_date=2009; citation_pages=908-914; citation_doi=10.1136/jcp.2009.067298; citation_id=CR15 citation_journal_title=Biochem Biophys Res Commun; citation_title=Human ZHX1: cloning, chromosomal location, and interaction with transcription factor NF-Y; citation_author=K Yamada, RL Printz, H Osawa, DK Granner; citation_volume=261; citation_publication_date=1999; citation_pages=614-621; citation_doi=10.1006/bbrc.1999.1087; citation_id=CR16 citation_journal_title=J Cell Biochem; citation_title=The SUMOylation of zinc-fingers and homeoboxes 1 (ZHX1) by Ubc9 regulates its stability and transcriptional repression activity; citation_author=S Chen, X Yu, Q Lei, L Ma, D Guo; citation_volume=114; citation_publication_date=2013; citation_pages=2323-2333; citation_doi=10.1002/jcb.24579; citation_id=CR17 citation_journal_title=Biochem Biophys Res Commun; citation_title=Zinc-fingers and homeoboxes 1 (ZHX1) binds DNA methyltransferase (DNMT) 3B to enhance DNMT3B-mediated transcriptional repression; citation_author=SH Kim, J Park, MC Choi, HP Kim, JH Park, Y Jung, JH Lee, DY Oh, SA Im, YJ Bang, TY Kim; citation_volume=355; citation_publication_date=2007; citation_pages=318-323; citation_doi=10.1016/j.bbrc.2007.01.187; citation_id=CR18 citation_journal_title=FEBS Lett; citation_title=Identification of proteins that interact with NF-YA; citation_author=K Yamada, H Osawa, DK Granner; citation_volume=460; citation_publication_date=1999; citation_pages=41-45; citation_doi=10.1016/S0014-5793(99)01311-3; citation_id=CR19 citation_journal_title=Kidney Int; citation_title=Early changes in gene expression that influence the course of primary glomerular disease; citation_author=LC Clement, G Liu, I Perez-Torres, YS Kanwar, C Avila-Casado, SS Chugh; citation_volume=72; citation_publication_date=2007; citation_pages=337-347; citation_doi=10.1038/sj.ki.5002302; citation_id=CR20 citation_journal_title=J Biol Chem; citation_title=ZHX proteins regulate podocyte gene expression during the development of nephrotic syndrome; citation_author=G Liu, LC Clement, YS Kanwar, C Avila-Casado, SS Chugh; citation_volume=281; citation_publication_date=2006; citation_pages=39681-39692; citation_doi=10.1074/jbc.M606664200; citation_id=CR21 citation_journal_title=Cell Mol Life Sci; citation_title=Three classes of C2H2 zinc finger proteins; citation_author=S Iuchi; citation_volume=58; citation_publication_date=2001; citation_pages=625-635; citation_doi=10.1007/PL00000885; citation_id=CR22 citation_journal_title=Biochem Biophys Res Commun; citation_title=Functional analysis and the molecular dissection of zinc-fingers and homeoboxes 1 (ZHX1); citation_author=K Yamada, H Kawata, K Matsuura, Z Shou, S Hirano, T Mizutani, T Yazawa, M Yoshino, T Sekiguchi, T Kajitani, K Miyamoto; citation_volume=297; citation_publication_date=2002; citation_pages=368-374; citation_doi=10.1016/S0006-291X(02)02203-9; citation_id=CR23 citation_journal_title=Biochem J; citation_title=Analysis of zinc-fingers and homeoboxes (ZHX)-1-interacting proteins: molecular cloning and characterization of a member of the ZHX family, ZHX3; citation_author=K Yamada, H Kawata, Z Shou, S Hirano, T Mizutani, T Yazawa, T Sekiguchi, M Yoshino, T Kajitani, K Miyamoto; citation_volume=373; citation_publication_date=2003; citation_pages=167-178; citation_doi=10.1042/BJ20021866; citation_id=CR24 citation_journal_title=Biochemistry; citation_title=The tandem zinc-finger region of human ZHX adopts a novel C2H2 zinc finger structure with a C-terminal extension; citation_author=H Wienk, I Lammers, A Hotze, J Wu, RW Wechselberger, R Owens, DK Stammers, D Stuart, R Kaptein, GE Folkers; citation_volume=48; citation_publication_date=2009; citation_pages=4431-4439; citation_doi=10.1021/bi9001997; citation_id=CR25 citation_journal_title=BMC Struct Biol; citation_title=Novel structural features in two ZHX homeodomains derived from a systematic study of single and multiple domains; citation_author=L Bird, J Ren, J Nettleship, G Folkers, R Owens, D Stammers; citation_volume=10; citation_publication_date=2010; citation_pages=13; citation_doi=10.1186/1472-6807-10-13; citation_id=CR26 citation_journal_title=J Steroid Biochem Mol Biol; citation_title=FLASH interacts with p160 coactivator subtypes and differentially suppresses transcriptional activity of steroid hormone receptors; citation_author=T Kino, T Ichijo, GP Chrousos; citation_volume=92; citation_publication_date=2004; citation_pages=357-363; citation_doi=10.1016/j.jsbmb.2004.09.003; citation_id=CR27 citation_journal_title=Proc Natl Acad Sci USA; citation_title=FLASH is required for histone transcription and S-phase progression; citation_author=D Barcaroli, L Bongiorno-Borbone, A Terrinoni, TG Hofmann, M Rossi, RA Knight, AG Matera, G Melino, V Laurenzi; citation_volume=103; citation_publication_date=2006; citation_pages=14808-14812; citation_doi=10.1073/pnas.0604227103; citation_id=CR28 citation_journal_title=EMBO J; citation_title=FLASH links the CD95 signaling pathway to the cell nucleus and nuclear bodies; citation_author=K Milovic-Holm, E Krieghoff, K Jensen, H Will, TG Hofmann; citation_volume=26; citation_publication_date=2007; citation_pages=391-401; citation_doi=10.1038/sj.emboj.7601504; citation_id=CR29 citation_journal_title=Leuk Res; citation_title=CASP8AP2 is a promising prognostic indicator in pediatric acute lymphoblastic leukemia; citation_author=Y Jiao, L Cui, C Gao, W Li, X Zhao, S Liu, M Wu, G Deng, Z Li; citation_volume=36; citation_publication_date=2012; citation_pages=67-71; citation_doi=10.1016/j.leukres.2011.05.023; citation_id=CR30 citation_journal_title=Blood; citation_title=Genes contributing to minimal residual disease in childhood acute lymphoblastic leukemia: prognostic significance of CASP8AP2; citation_author=C Flotho, E Coustan-Smith, D Pei, S Iwamoto, G Song, C Cheng, CH Pui, JR Downing, D Campana; citation_volume=108; citation_publication_date=2006; citation_pages=1050-1057; citation_doi=10.1182/blood-2006-01-0322; citation_id=CR31 citation_journal_title=Mol Cell Biol; citation_title=Interaction of FLASH with arsenite resistance protein 2 is involved in cell cycle progression at S phase; citation_author=M Kiriyama, Y Kobayashi, M Saito, F Ishikawa, S Yonehara; citation_volume=29; citation_publication_date=2009; citation_pages=4729-4741; citation_doi=10.1128/MCB.00289-09; citation_id=CR32 citation_journal_title=J Biol Chem; citation_title=Tumor necrosis factor alpha receptor- and Fas-associated FLASH inhibit transcriptional activity of the glucocorticoid receptor by binding to and interfering with its interaction with p160 type nuclear receptor coactivators; citation_author=T Kino, GP Chrousos; citation_volume=278; citation_publication_date=2003; citation_pages=3023-3029; citation_doi=10.1074/jbc.M209234200; citation_id=CR33 citation_journal_title=Mol Cell Proteomics; citation_title=Targeting the human cancer pathway protein interaction network by structural genomics; citation_author=YJ Huang, D Hang, LJ Lu, L Tong, MB Gerstein, GT Montelione; citation_volume=7; citation_publication_date=2008; citation_pages=2048-2060; citation_doi=10.1074/mcp.M700550-MCP200; citation_id=CR34 citation_journal_title=Methods Enzymol; citation_title=Robotic cloning and protein production platform of the Northeast Structural Genomics Consortium; citation_author=TB Acton, KC Gunsalus, R Xiao, LC Ma, J Aramini, MC Baran, YW Chiang, T Climent, B Cooper, NG Denissova, SM Douglas, JK Everett, CK Ho, D Macapagal, PK Rajan, R Shastry, LY Shih, GVT Swapna, M Wilson, M Wu, M Gerstein, M Inouye, JF Hunt, GT Montelione; citation_volume=394; citation_publication_date=2005; citation_pages=210-243; citation_doi=10.1016/S0076-6879(05)94008-1; citation_id=CR35 citation_journal_title=Methods Enzymol; citation_title=Preparation of protein samples for NMR structure, function, and small-molecule screening studies; citation_author=TB Acton, R Xiao, S Anderson, J Aramini, WA Buchwald, C Ciccosanti, K Conover, J Everett, K Hamilton, YJ Huang, H Janjua, G Kornhaber, J Lau, DY Lee, GH Liu, M Maglaqui, LC Ma, L Mao, D Patel, P Rossi, S Sahdev, R Shastry, GVT Swapna, YF Tang, SC Tong, DY Wang, H Wang, L Zhao, GT Montelione; citation_volume=493; citation_publication_date=2011; citation_pages=21-60; citation_doi=10.1016/B978-0-12-381274-2.00002-9; citation_id=CR36 citation_journal_title=J Struct Biol; citation_title=The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium; citation_author=R Xiao, S Anderson, J Aramini, R Belote, WA Buchwald, C Ciccosanti, K Conover, JK Everett, K Hamilton, YJ Huang, H Janjua, M Jiang, GJ Kornhaber, DY Lee, JY Locke, LC Ma, M Maglaqui, L Mao, S Mitra, D Patel, P Rossi, S Sahdev, S Sharma, R Shastry, GVT Swapna, SN Tong, D Wang, H Wang, L Zhao, GT Montelione, TB Acton; citation_volume=172; citation_publication_date=2010; citation_pages=21-33; citation_doi=10.1016/j.jsb.2010.07.011; citation_id=CR37 citation_journal_title=Biochemistry; citation_title=Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling; citation_author=D Neri, T Szyperski, G Otting, H Senn, K Wuthrich; citation_volume=28; citation_publication_date=1989; citation_pages=7510-7516; citation_doi=10.1021/bi00445a003; citation_id=CR38 citation_journal_title=Methods Enzymol; citation_title=Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data; citation_author=HNB Moseley, D Monleon, GT Montelione; citation_volume=339; citation_publication_date=2001; citation_pages=91-108; citation_doi=10.1016/S0076-6879(01)39311-4; citation_id=CR39 citation_journal_title=J Mol Biol; citation_title=Automated analysis of protein NMR assignments using methods from artificial intelligence; citation_author=DE Zimmerman, CA Kulikowski, YP Huang, WQ Feng, M Tashiro, S Shimotakahara, CY Chien, R Powers, GT Montelione; citation_volume=269; citation_publication_date=1997; citation_pages=592-610; citation_doi=10.1006/jmbi.1997.1052; citation_id=CR40 citation_journal_title=J Am Chem Soc; citation_title=Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics; citation_author=YJ Huang, R Powers, GT Montelione; citation_volume=127; citation_publication_date=2005; citation_pages=1665-1674; citation_doi=10.1021/ja047109h; citation_id=CR41 citation_journal_title=Proc Natl Acad Sci USA; citation_title=NMR data collection and analysis protocol for high-throughput protein structure determination; citation_author=G Liu, Y Shen, HS Atreya, D Parish, Y Shao, DK Sukumaran, R Xiao, A Yee, A Lemak, A Bhattacharya, TA Acton, CH Arrowsmith, GT Montelione, T Szyperski; citation_volume=102; citation_publication_date=2005; citation_pages=10487-10492; citation_doi=10.1073/pnas.0504338102; citation_id=CR42 citation_journal_title=J Mol Biol; citation_title=Torsion angle dynamics for NMR structure calculation with the new program DYANA; citation_author=P Güntert, C Mumenthaler, K Wüthrich; citation_volume=273; citation_publication_date=1997; citation_pages=283-298; citation_doi=10.1006/jmbi.1997.1284; citation_id=CR43 citation_journal_title=J Mol Biol; citation_title=Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA; citation_author=T Herrmann, P Güntert, K Wüthrich; citation_volume=319; citation_publication_date=2002; citation_pages=209-227; citation_doi=10.1016/S0022-2836(02)00241-3; citation_id=CR44 citation_journal_title=Proteins; citation_title=A topology-constrained distance network algorithm for protein structure determination from NOESY data; citation_author=YJ Huang, R Tejero, R Powers, GT Montelione; citation_volume=62; citation_publication_date=2006; citation_pages=587-603; citation_doi=10.1002/prot.20820; citation_id=CR45 citation_journal_title=J Biomol NMR; citation_title=Protein backbone angle restraints from searching a database for chemical shift and sequence homology; citation_author=G Cornilescu, F Delaglio, A Bax; citation_volume=13; citation_publication_date=1999; citation_pages=289-302; citation_doi=10.1023/A:1008392405740; citation_id=CR46 citation_journal_title=Acta Crystallogr Sect D: Biol Crystallogr; citation_title=Crystallography & NMR system: a new software suite for macromolecular structure determination; citation_author=AT Brunger, PD Adams, GM Clore, WL DeLano, P Gros, RW Grosse-Kunstleve, JS Jiang, J Kuszewski, M Nilges, NS Pannu, RJ Read, LM Rice, T Simonson, GL Warren; citation_volume=54; citation_publication_date=1998; citation_pages=905-921; citation_doi=10.1107/S0907444998003254; citation_id=CR47 citation_journal_title=Proteins ; citation_title=Evaluating protein structures determined by structural genomics consortia; citation_author=A Bhattacharya, R Tejero, GT Montelione; citation_volume=66; citation_publication_date=2007; citation_pages=778-795; citation_doi=10.1002/prot.21165; citation_id=CR48 citation_journal_title=Nucleic Acids Res; citation_title=The protein data bank; citation_author=HM Berman, J Westbrook, Z Feng, G Gilliland, TN Bhat, H Weissig, IN Shindyalov, PE Bourne; citation_volume=28; citation_publication_date=2000; citation_pages=235-242; citation_doi=10.1093/nar/28.1.235; citation_id=CR49 citation_journal_title=Annu Rev Biochem; citation_title=Homeodomain proteins; citation_author=WJ Gehring, M Affolter, T Burglin; citation_volume=63; citation_publication_date=1994; citation_pages=487-526; citation_doi=10.1146/annurev.bi.63.070194.002415; citation_id=CR50 citation_journal_title=Trends Biochem Sci; citation_title=Dali: a network tool for protein structure comparison; citation_author=L Holm, C Sander; citation_volume=20; citation_publication_date=1995; citation_pages=478-480; citation_doi=10.1016/S0968-0004(00)89105-7; citation_id=CR51 citation_journal_title=The EMBO Journal; citation_title=Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless; citation_author=K Miyazono, Y Zhi, Y Takamura, K Nagata, K Saigo, T Kojima, M Tanokura; citation_volume=29; citation_publication_date=2010; citation_pages=1613-1623; citation_doi=10.1038/emboj.2010.53; citation_id=CR52 citation_journal_title=J Biol Chem; citation_title=Site-specific heterodimerization by paired-class homeodomain proteins mediates selective transcriptional responses; citation_author=SC Tucker, R Wisdom; citation_volume=274; citation_publication_date=1999; citation_pages=32325-32332; citation_doi=10.1074/jbc.274.45.32325; citation_id=CR53 citation_journal_title=Dev Biol; citation_title=A concerted action of a paired-type homeobox gene, aristaless, and a homolog of Hox11/tlx homeobox gene, clawless, is essential for the distal tip development of the Drosophila leg; citation_author=T Kojima, T Tsuji, K Saigo; citation_volume=279; citation_publication_date=2005; citation_pages=434-445; citation_doi=10.1016/j.ydbio.2004.12.005; citation_id=CR54 citation_journal_title=Nature; citation_title=Interaction between two homeodomain proteins is specified by a short C-terminal tail; citation_author=MR Stark, AD Johnson; citation_volume=371; citation_publication_date=1994; citation_pages=429-432; citation_doi=10.1038/371429a0; citation_id=CR55 citation_journal_title=J Biomol NMR; citation_title=Assignment validation software suite for the evaluation and presentation of protein resonance assignment data; citation_author=HNB Moseley, G Sahota, GT Montelione; citation_volume=28; citation_publication_date=2004; citation_pages=341-355; citation_doi=10.1023/B:JNMR.0000015420.44364.06; citation_id=CR56