PDBsum entry 3f8t

Hydrolase

PDB id: 3f8t

Contents

Protein chain

459 a.a. *

Waters ×237

* Residue conservation analysis

PDB id:

3f8t

Name:

Hydrolase

Title:

Crystal structure analysis of a full-length mcm homolog from methanopyrus kandleri

Structure:

Predicted atpase involved in replication control, cdc46/mcm family. Chain: a. Engineered: yes

Source:

Methanopyrus kandleri av19. Organism_taxid: 190192. Strain: av19 / dsm 6324 / jcm 9639 / nbrc 100938. Gene: mcm2_2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.214 R-free: 0.251

Authors:

B.Bae,S.K.Nair

Key ref:

B.Bae et al. (2009). Insights into the architecture of the replicative helicase from the structure of an archaeal MCM homolog. Structure, 17, 211-222. PubMed id: 19217392 DOI: 10.1016/j.str.2008.11.010

Date:

13-Nov-08 Release date: 03-Mar-09

Protein chain

Q8TWB5  (Q8TWB5_METKA) -  Predicted ATPase involved in replication control, Cdc46/Mcm family from Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)

Seq: 506 a.a.

Struc: 459 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1016/j.str.2008.11.010

Structure 17:211-222 (2009)

PubMed id: 19217392

Insights into the architecture of the replicative helicase from the structure of an archaeal MCM homolog.

B.Bae, Y.H.Chen, A.Costa, S.Onesti, J.S.Brunzelle, Y.Lin, I.K.Cann, S.K.Nair.

ABSTRACT

The minichromosome maintenance (MCM) proteins, members of the AAA+ (ATPase associated with diverse cellular activities) superfamily, are believed to constitute the replicative helicase in eukaryotic and archaeal species. Here, we present the 1.9 A resolution crystal structure of a monomeric MCM homolog from Methanopyrus kandleri, the first crystallographic structure of a full-length MCM. We also present an 18 A cryo-electron microscopy reconstruction of the hexameric MCM from Methanothermobacter thermautotrophicus, and fit the atomic resolution crystal structure into the reconstruction in order to generate an atomic model for the oligomeric assembly. These structural data reveal a distinct active site topology consisting of a unique arrangement of critical determinants. The structures also provide a molecular framework for understanding the functional contributions of trans-acting elements that facilitate intersubunit crosstalk in response to DNA binding and ATP hydrolysis.

Selected figure(s)

Figure 3.
Figure 3. Cryo-EM Density Map of the MCM Hexamer
(A and C) Surface rendering of the cryo-EM density map (displayed at 2σ) viewed from the top and the side, respectively. The side view clearly shows the lateral holes, which are disrupted by an isthmus of electron density.
(B and D) Fitting of the AAA+ domain from MkaMCM2 (red) and the N-terminal domain from MthMCM (green, Fletcher et al., 2003). The AAA+ domain of MkaMCM2 matches well the dome-shaped electron density.
(E) A view showing the fitting of two hybrid monomers (including the N-terminal domain of MthMCM and the AAA+ domain of MkaMCM2). The N-terminal domain of one subunit (highlighted in green) communicates with the AAA+ domain of the next-neighboring subunit (in red) through the interaction between the PS1BH of the AAA+ domain (shown in yellow) and the β7-β8 loop of the N-terminal domain of an adjacent subunit (in orange) consistent with biochemical studies on MthMCM (Sakakibara et al., 2008).
(F) A close up of the same interaction.

Figure 4.
Figure 4. Unique Trans-Acting Residues Characterize the MCM AAA+ Domain
(A) Model of the MCM hexamer derived as per Figure 3B showing the location of the composite active site formed between two AAA+ domains (colored in blue and red).
(B) A close up view of the composite active site showing residues that have been demonstrated to be critical for ATP hydrolysis. The composite active site in MCM has unique features that distinguish the AAA+ modules of these proteins from classical AAA+ ATPases such as DnaA.
(C) Within the active site of DnaA (Erzberger et al., 2006), the Walker A and B motifs, sensor I and sensor II helix, are situated in one molecule as cis-acting elements, but the critical arginine finger is a trans-acting residue that is contributed from a neighboring subunit.
(D) In contrast, the sensor II helix in MCM functions in trans and is contributed by a neighboring subunit.
(E–H) This arrangement of trans-acting elements is similar to that found in viral superfamily III helicases, such as the papillomavirus E1 helicase (Enemark and Joshua-Tor, 2006) (E). An additional trans-site has been identified by biochemical analysis of SsoMCM (Moreau et al., 2007) and consists of a motif containing a highly conserved acidic residue at the base of PS1BH. Comparison of the structure of the SV40 large T antigen bound to (F) ATP and (G) ADP demonstrates that this acidic residue orients the arginine finger in response to the nature of the nucleotide (Gai et al., 2004). Likewise, a similar, highly conserved acidic residue is located as a trans-element in MCM (H) where it might similarly affect intersubunit association in response to nucleotide hydrolysis.

The above figures are reprinted by permission from Cell Press: Structure (2009, 17, 211-222) copyright 2009.

Figures were selected by an automated process.