1vya

Identification and characterization of the first plant G-quadruplex binding protein encoded by the Zea mays L. nucleoside diphosphate1 gene, ZmNDPK1

spinqualitylabelsall models 1vya, resolution 2.05Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1vya is a 12 chain structure with sequence from Zea mays. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.05Å Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function NDK1_MAIZE Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity). Involved in transcription regulation (Probable). Has G-quadruplex (G4) DNA-binding activity, which is independent of its nucleotide-binding and kinase activity. Binds folded G4 with low nanomolar affinity and corresponding unfolded G-rich DNA more weakly. Stabilizes folded G4s regardless of whether they are prefolded or not (PubMed:25679041).[UniProtKB:P36010] Publication Abstract from PubMed Noncanonical forms of DNA like the guanine quadruplex (G4) play important roles in regulating transcription and translation through interactions with their protein partners. Although potential G4 elements have been identified in or near genes from species diverse as bacteria, mammals, and plants, little is known about how they might function as cis-regulatory elements or as binding sites for trans-acting protein partners. In fact, until now no G4 binding partners have been identified in the plant kingdom. Here, we report on the cloning and characterization of the first plant-kingdom gene known to encode a G4-binding protein, maize (Zea mays L.) nucleoside diphosphate kinase1 (ZmNDPK1). Structural characterization by X-ray crystallography reveals that it is a homohexamer, akin to other known NDPKs like the human homologue NM23-H2. Further probing into the G4-binding properties of both NDPK homologues suggests that ZmNDPK1 possesses properties distinct from that of NM23-H2, which is known to interact with a G-rich sequence element upstream of the c-myc gene and, in doing so, modulate its expression. Indeed, ZmNDPK1 binds the folded G4 with low nanomolar affinity but corresponding unfolded G-rich DNA more weakly, whereas NM23-H2 binds both folded and unfolded G4 with low nanomolar affinities; nonetheless, both homologues appear to stabilize folded DNAs whether they were prefolded or not. We also demonstrate that the G4-binding activity of ZmNDPK1 is independent of nucleotide binding and kinase activity, suggesting that the G4-binding region and the enzyme active sites are separate. Together, these findings establish a broad evolutionary conservation of some NDPKs as G4-DNA binding enzymes, but with potentially distinct biochemical properties that may reflect divergent evolution or species-specific deployment of these elements in gene regulatory processes. The Maize (Zea mays L.) Nucleoside Diphosphate Kinase1 (ZmNDPK1) Gene Encodes a Human NM23-H2 Homologue That Binds and Stabilizes G-Quadruplex DNA.,Kopylov M, Bass HW, Stroupe ME Biochemistry. 2015 Mar 10;54(9):1743-57. doi: 10.1021/bi501284g. Epub 2015 Feb, 24. PMID:25679041 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Nucleoside diphosphate kinase 3D structures

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