3LDB

Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment.

Summary for 3LDB

• Entry DOI: 10.2210/pdb3ldb/pdb
• Related: 3LD8
• Descriptor: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6, antibody Fab fragment light chain, antibody Fab fragment heavy chain, ... (8 entities in total)
• Functional Keywords: jmj6d, alpha-ketoglutarate, fab fragments, immune system
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus, nucleoplasm: Q6NYC1
• Total number of polymer chains: 3
• Total formula weight: 90434.20

Authors

Hong, X.,Zang, J.,White, J.,Kappler, J.W.,Wang, C.,Zhang, G. (deposition date: 2010-01-12, release date: 2010-08-04, Last modification date: 2024-10-09)

Primary citation

Hong, X.,Zang, J.,White, J.,Wang, C.,Pan, C.H.,Zhao, R.,Murphy, R.C.,Dai, S.,Henson, P.,Kappler, J.W.,Hagman, J.,Zhang, G.
Interaction of JMJD6 with single-stranded RNA.
Proc.Natl.Acad.Sci.USA, 107:14568-14572, 2010

PubMed Abstract: JMJD6 is a Jumonji C domain-containing hydroxylase. JMJD6 binds alpha-ketoglutarate and iron and has been characterized as either a histone arginine demethylase or U2AF65 lysyl hydroxylase. Here, we describe the structures of JMJD6 with and without alpha-ketoglutarate, which revealed a novel substrate binding groove and two positively charged surfaces. The structures also contain a stack of aromatic residues located near the active center. The side chain of one residue within this stack assumed different conformations in the two structures. Interestingly, JMJD6 bound efficiently to single-stranded RNA, but not to single-stranded DNA, double-stranded RNA, or double-stranded DNA. These structural features and truncation analysis of JMJD6 suggest that JMJD6 may bind and modify single-stand RNA rather than the previously reported peptide substrates.

PubMed: 20679243
DOI: 10.1073/pnas.1008832107

Experimental method

X-RAY DIFFRACTION (2.7 Å)