PDBsum entry 2c9o

Hydrolase

PDB id: 2c9o

Contents

Protein chains

398 a.a. *

311 a.a. *

Ligands

ADP ×3

Waters ×158

* Residue conservation analysis

PDB id:

2c9o

Name:

Hydrolase

Title:

3d structure of the human ruvb-like helicase ruvbl1

Structure:

Ruvb-like 1. Chain: a, b, c. Synonym: ruvbl1,49-kda tata box-binding protein-interacting protein, 49 kda tbp-interacting protein, tip49a, pontin 52,nuclear matrix protein 238,nmp 238,54 kda erythrocyte cytosolic protein, ecp-54, tip60-associated protein 54-alpha, tap54-alpha. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.20Å R-factor: 0.209 R-free: 0.257

Authors:

P.M.Matias,S.Gorynia,P.Donner,M.A.Carrondo

Key ref:

P.M.Matias et al. (2006). Crystal structure of the human AAA+ protein RuvBL1. J Biol Chem, 281, 38918-38929. PubMed id: 17060327 DOI: 10.1074/jbc.M605625200

Date:

14-Dec-05 Release date: 23-Oct-06

Protein chains

Q9Y265  (RUVB1_HUMAN) -  RuvB-like 1 from Homo sapiens

Seq: 456 a.a.

Struc: 398 a.a.

Protein chain

Q9Y265  (RUVB1_HUMAN) -  RuvB-like 1 from Homo sapiens

Seq: 456 a.a.

Struc: 311 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M605625200

J Biol Chem 281:38918-38929 (2006)

PubMed id: 17060327

Crystal structure of the human AAA+ protein RuvBL1.

P.M.Matias, S.Gorynia, P.Donner, M.A.Carrondo.

ABSTRACT

RuvBL1 is an evolutionarily highly conserved eukaryotic protein belonging to the AAA(+)-family of ATPases (ATPase associated with diverse cellular activities). It plays important roles in essential signaling pathways such as the c-Myc and Wnt pathways in chromatin remodeling, transcriptional and developmental regulation, and DNA repair and apoptosis. Herein we present the three-dimensional structure of the selenomethionine variant of human RuvBL1 refined using diffraction data to 2.2A of resolution. The crystal structure of the hexamer is formed of ADP-bound RuvBL1 monomers. The monomers contain three domains, of which the first and the third are involved in ATP binding and hydrolysis. Although it has been shown that ATPase activity of RuvBL1 is needed for several in vivo functions, we could only detect a marginal activity with the purified protein. Structural homology and DNA binding studies demonstrate that the second domain, which is unique among AAA(+) proteins and not present in the bacterial homolog RuvB, is a novel DNA/RNA-binding domain. We were able to demonstrate that RuvBL1 interacted with single-stranded DNA/RNA and double-stranded DNA. The structure of the RuvBL1.ADP complex, combined with our biochemical results, suggest that although RuvBL1 has all the structural characteristics of a molecular motor, even of an ATP-driven helicase, one or more as yet undetermined cofactors are needed for its enzymatic activity.

Selected figure(s)

Figure 2.
FIGURE 2. The DNA binding region in RuvBL1 domain II. A, stereoview of the protein C^ trace (gold) and ssDNA ball-and-stick representation (carbon, nitrogen, oxygen, and phosphorus atoms are colored gray, blue, red, and green, respectively) of the RPA molecule (PDB 1JMC) superimposed onto the DNA binding region of RuvBL1 DII (residues 127-233; cyan). The long loops in the N-terminal domain of RPA that interact with ssDNA (arrows 1 and 3) correspond to a disordered loop and a much shorter loop (arrow 2) in RuvBL1 DII. B, view of the electrostatic potential of the RPA molecule mapped at its molecular surface. The molecular surface was calculated with MSMS (65) using a probe radius of 1.4 Å, and the electrostatic potential was calculated with MEAD (66) using an ionic strength of 0.1 M, dielectric constants of 4.0 and 80.0 for the protein and the exterior, respectively, and a temperature of 300 K. The range of potentials shown spans -5 (red) to +5 kT/e (blue) units. C, view of the electrostatic potential of the DNA binding region of RuvBL1 DII mapped at its molecular surface. The molecular surface and the electrostatic potential were calculated as described above for the whole RuvBL1 hexamer, but for clarity only the DNA binding region of RuvBL1 DII is represented. As a visual aid, the ssDNA molecule bound to RPA is represented in ball-and-stick (Carbon, nitrogen, oxygen, and phosphorus atoms are colored gray, blue, red, and green, respectively). The view in B and C is the same as in Fig. 2A. Drawings were prepared with DINO.

Figure 3.
FIGURE 3. The RuvBL1 hexamer. A, ribbon diagram of the RuvBL1 hexamer (side view). Adjacent monomers are colored light gray and gold. One gold monomer is colored in the same way as in Fig. 1B to highlight its domain structure. The hexamer herein represented is the crystallographic hexamer, formed by monomers A around the crystallographic 6-fold axis. The bound ADP molecules are depicted in space-filling mode, where each atom is represented by a sphere with a diameter twice its conventional van der Waals radius. Carbon, nitrogen, oxygen, and phosphorus atoms are colored gray, blue, red, and green, respectively. B, ribbon diagram of the RuvBL1 hexamer (top view). The coloring scheme is as in A. Drawings were prepared with DINO.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 38918-38929) copyright 2006.

Figures were selected by the author.