PDBsum entry 2a23

Recombination

PDB id

2a23

Contents

			Protein chain

					82 a.a.

			Metals

					_ZN ×2

References listed in PDB file

Key reference

Title

A phd finger motif in the c terminus of rag2 modulates recombination activity.

Authors

S.K.Elkin, D.Ivanov, M.Ewalt, C.G.Ferguson, S.G.Hyberts, Z.Y.Sun, G.D.Prestwich, J.Yuan, G.Wagner, M.A.Oettinger, O.P.Gozani.

Ref.

J Biol Chem, 2005, 280, 28701-28710. [DOI no: 10.1074/jbc.M504731200]

PubMed id

15964836

Abstract

The RAG1 and RAG2 proteins catalyze V(D)J recombination and are essential for generation of the diverse repertoire of antigen receptor genes and effective immune responses. RAG2 is composed of a "core" domain that is required for the recombination reaction and a C-terminal nonessential or "non-core" region. Recent evidence has emerged arguing that the non-core region plays a critical regulatory role in the recombination reaction, and mutations in this region have been identified in patients with immunodeficiencies. Here we present the first structural data for the RAG2 protein, using NMR spectroscopy to demonstrate that the C terminus of RAG2 contains a noncanonical PHD finger. All of the non-core mutations of RAG2 that are implicated in the development of immunodeficiencies are located within the PHD finger, at either zinc-coordinating residues or residues adjacent to an alpha-helix on the surface of the domain that participates in binding to the signaling molecules, phosphoinositides. Functional analysis of disease and phosphoinositide-binding mutations reveals novel intramolecular interactions within the non-core region and suggests that the PHD finger adopts two distinct states. We propose a model in which the equilibrium between these states modulates recombination activity. Together, these data identify the PHD finger as a novel and functionally important domain of RAG2.



	Figure 2. FIG. 2. The RAG2 C terminus contains a noncanonical PHD finger. A, alignment of the RAG2 zinc finger to representative zinc fingers from similar structural classes. The RAG2 sequence (aa 414-487) was aligned to the indicated PHD, RING, and FYVE finger sequences. Red circles represent zinc-binding residues Cys-419, His-452, and His-481 of RAG2 that deviate from the PHD finger consensus. Zn1, first zinc; Zn2, second zinc; L1 and L2, extended segments of sequence between pairs of zinc-coordinating residues. B, the RAG2 zinc finger is structurally most similar to the PHD finger. Ribbon schematics compare the C-terminal zinc finger of RAG2 to the indicated PHD, RING, and FIVE fingers. The ligands of the two zinc ions appear as interleaved pairs in the primary sequence of these proteins as shown in A. Two extended polypeptide segments (L1 and L2, see A) separate equivalent pairs of zinc-coordinating residues. The L1 segment contains the first strand of the conserved -sheet, whereas the conformation of L2 varies significantly between different proteins. The four domains are oriented in the same way using conserved -sheet and zinc ions as structural reference. The L2 -helix of RAG2 is denoted in blue. Yellow, zinc-coordinating cysteine residues; blue, zinc-coordinating histidine residues; red spheres, zinc atoms.		Figure 4. FIG. 4. Model of RAG2-PtdInsP interactions. A, structural overlay of the RAG2 PHD finger (green) on the EEA1 FYVE finger-IP(1,3)[2] complex (FYVE domain, magenta; inositol 1,3-P[2], yellow). (Protein Data Bank code 1HYI [PDB] (46).) The conserved -sheet and zinc ions were used to overlay the two structures. Arginine side chains important for FYVE-PtdInsP binding are shown in magenta. Basic residues of RAG2 in the L2 segment (Arg-464 and His-468) are shown in blue. B, ribbon schematic of the RAG2 PHD finger structure with the indicated basic residues (blue) and disease-linked residues (red). C, schematic comparison of RAG2 and ING2 C termini. PHD fingers are shown in green. The blue boxes denote regions of positively charged residues important for PtdInsP binding by ING2. The analogous regions of RAG2 (L2 and CT) are also highlighted in blue, with the one inside the PHD finger (L2) corresponding to the blue -helix region in B.

PROCHECK

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