Crystal Structure of the Human NKX2.5 Homeodomain in Complex with DNA Target

Pradhan, Lagnajeet; Genis, Caroli; Scone, Peyton; Weinberg, Ellen O.; Kasahara, Hideko; Nam, Hyun Joo

doi:10.1021/bi300849c

Cited by 42 publications

(66 citation statements)

References 57 publications

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“…In addition to the HD, NKX2.5 contains N-and C-terminal regulatory domains. The HD is centrally located at amino acid positions 138-197 and is involved in nuclear translocation and interaction with other transcription factors as well as DNA binding (59). The NKX2.5 mutation of p.F145S identified in this study is located in HD, and may thus be expected to exert influence on the transcriptional activity of NKX2.5 by interfering with its nuclear distribution or DNA-binding ability.…”

Section: Discussionmentioning

confidence: 80%

A novel NKX2.5 loss-of-function mutation responsible for familial atrial fibrillation

Huang

Xue

et al. 2013

International Journal of Molecular Medicine

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Abstract. Atrial fibrillation (AF) represents the most common form of sustained cardiac arrhythmia and accounts for substantial morbidity and mortality. Increasing evidence demonstrates that abnormal cardiovascular development is involved in the pathogenesis of AF. In this study, the coding exons and splice sites of the NKX2.5 gene, which encodes a homeodomain-containing transcription factor pivotal for normal cardiovascular morphogenesis, were sequenced in 110 unrelated index patients with familial AF. The available relatives of the mutation carrier and 200 unrelated ethnically-matched healthy individuals serving as controls were subsequently genotyped. The disease-causing potential of the identified NKX2.5 variation was predicted by MutationTaster. The functional characteristics of the mutant NKX2.5 protein were analyzed using a dual-luciferase reporter assay system. As a result, a novel heterozygous NKX2.5 mutation, p.F145S, was identified in a family with AF transmitted as an autosomal dominant trait, which co-segregated with AF in the family with complete penetrance. The detected substitution, which altered the amino acid completely conserved evolutionarily across species, was absent in 400 control chromosomes and was automatically predicted to be causative. Functional analysis demonstrated that the NKX2.5 mutant was associated with significantly decreased transcriptional activity compared with its wild-type counterpart. To the best of our knowledge, this is the first report on the association of the NKX2.5 lossof-function mutation with increased susceptibility to familial AF. The findings of the present study provide novel insights into the molecular mechanism underlying AF, suggesting the potential implications for the early prophylaxis and allelespecific therapy of AF.

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Section: Discussionmentioning

confidence: 80%

A novel NKX2.5 loss-of-function mutation responsible for familial atrial fibrillation

Huang

Xue

et al. 2013

International Journal of Molecular Medicine

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“…The aminoterminal and carboxy-terminal domains contain regulatory elements involved in interactions with other transcription factors or transcription machinery. The binary complex structures of NKX2.5 HD in complex with DNA and TBX5 TBD with DNA have previously been reported (Pradhan et al, 2012;Stirnimann et al, 2010).…”

Section: Introductionmentioning

confidence: 88%

“…Cloning of the NKX2.5 HD expression construct and purification of the protein have previously been reported (Genis et al, 2008;Pradhan et al, 2012). The DNA coding amino acids 58-238 of TBX5 protein was cloned between the NdeI and BamHI sites of pET28 vector (Novagen).…”

Section: Protein Expression and Purificationmentioning

confidence: 99%

“…A molecular-replacement search was performed using the NKX2.5 HD (PDB entry 3rkq, Pradhan et al, 2012) and TBX5 TBD (PDB entry 2x6v, Stirnimann et al, 2010) as search models. The program et al, 2007) was used for the search and the structure was refined using the PHENIX suite.…”

Section: X-ray Data Collection Processing and Preliminary Structure mentioning

confidence: 99%

“…The phases for the data were determined by molecular replacement using NKX2.5 HD-DNA (Pradhan et al, 2012) and TBX5 TBD-DNA (Stirnimann et al, 2010) complex structures as search models and the program Phaser. Unambiguous solutions were obtained by searching the two TBX5 TBD solutions first (Z = 14.2 and 12.2, respectively) and then positioning NKX2.5 HD molecules (Z = 34.8 and 31.0, respectively).…”

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confidence: 99%

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Crystallization and preliminary X-ray analysis of the cardiac transcription factor complex of NKX2.5 and TBX5 with DNA

Pradhan¹,

Gopal²,

Nam³

2014

Acta Cryst Sect F

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Heart development depends on timely expression of genes regulated by combinatorial interactions of master cardiac transcription factors. To elucidate the molecular basis of their interactions, a ternary complex of cardiac transcription factors, NKX2.5 and TBX5, and their target DNA was studied using X-ray crystallography. Here, the purification, crystallization and preliminary X-ray crystallographic analyses of the NKX2.5 homeodomain and TBX5 DNA-binding domain complex with a DNA element from the À252 promoter region of the atrial natriuretic factor are reported. The crystal diffracted to 2.88 Å resolution and belonged to space group P2 1 , with unit-cell parameters a = 69.30, b = 77.78, c = 77.60 Å , = 108.31. Two sets of ternary complexes are present in an asymmetric unit with a solvent content of 54%.

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A de novo heterozygous HOXA11 variant in a patient with mesomelic dysplasia with urogenital abnormalities

Sezer

Perçin

Kazan

et al. 2022

American J of Med Genetics Pt A

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Mesomelic dysplasias are a genetically and clinically heterogeneous group of diseases with more than 10 types defined. This article presents an 18-year-old female patient with normal intelligence and a multisystem phenotype including disproportionate short stature, scoliosis, mesomelic limb shortening, radial bowing, short fourth to fifth metacarpals and metatarsals, fusions in the carpal/tarsal bones, operated pes equinovarus, primary amenorrhea, uterine hypoplasia, vesicoureteral reflux, and chronic kidney disease. Whole-exome sequencing revealed a de novo heterozygous c.881T>G (p.Met294Arg) variant in HOXA11 (NM_005523.6) gene. The variant was located in the homeodomain of HOXA11 and predicted to alter DNA-binding ability of the protein. In silico analyses indicated that the variant could promote the alterations in the protein-protein interaction. The possible functional effect of the variant was supposed as dominant-negative. Hoxa11-mutant mice have been reported to exhibit homeotic transformations in the thoracic and sacral vertebrae, zeugopodal phenotype in forelimb and hindlimb, and urogenital abnormalities. Although mice models were reported as mesomelic dysplasia and urogenital abnormalities (MDUGA), this phenotype has not yet been reported in humans. This was the first case with MDUGA putatively related to a de novo variant in HOXA11.

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Crystal Structure of the Human NKX2.5 Homeodomain in Complex with DNA Target

Cited by 42 publications

References 57 publications

A novel NKX2.5 loss-of-function mutation responsible for familial atrial fibrillation

A novel NKX2.5 loss-of-function mutation responsible for familial atrial fibrillation

Crystallization and preliminary X-ray analysis of the cardiac transcription factor complex of NKX2.5 and TBX5 with DNA

A de novo heterozygous HOXA11 variant in a patient with mesomelic dysplasia with urogenital abnormalities

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