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Cbikp Structure

Modified tetrapyrroles are key elements for life since they serve as cofactors and pigments in several biological processes. Well-known examples are hemes, siroheme, vitamin B12, coenzyme F430 and chlorophyll, whose assembly requires insertion of a specific metal ion into the tetrapyrrolic structure, via chelatase enzymes. Cobaltochelatases act in the vitamin B12 biosynthetic pathway, cobalt being inserted into the tetrapyrrole ring.

The X-Ray crystallographic structure from the cobaltchelatase CbiKP from Desulfovibrio vulgaris was determined, and this is the first structure of a cobalt-loaded cobaltochelatase revealing the aminoacid residues involved on the cobalt binding.

Furthermore, the protein structure revealed some new features on the chelatase superfamily: tetrameric oligomerization with a heme b cofactor located at the interface between two monomers. The tetramer is organized in such a way that a central cavity with the potential for ligand binding is formed. The structure suggests that the cobaltochelatase CbiKP of D. vulgaris may have evolved an additional function, such as the transport of metals across the periplasmic space.


C.V. Romão, D. Ladakis, S.A.L. Lobo, M.A. Carrondo, A.A. Brindley, E. Deery, P.M. Matias, R.W. Pickersgill, L.M. Saraiva and M.J. Warren, “Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization”, PNAS (2011), 108(1): 97-102



Last Updated on Monday, 22 August 2011 09:48

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SOR - Sulfur Oxigenase Reductase

SOR from the thermoacidophilic and chemolithotrophic archaeon A. ambivalens is the initial enzyme in its dissimilatory sulfur oxidation pathway. SOR is a self-compartment-alizing enzyme (308 aa) that disproportionates sulfur into H2S, SO32- and SSO32-, using a low-potential mono-nuclear non-heme iron centre as catalytic site, in a reaction where elemental sulfur works both as electron donor and acceptor.



Urich T, Coelho R, Kletzin A, Frazao C. The sulfur oxygenase reductase from Acidianus ambivalens is an icosatetramer as shown by crystallization and Patterson analysis. Biochim Biophys Acta. 2005 Mar 14;1747(2):267-70.

Urich T, Gomes CM, Kletzin A, Frazão C. X-ray Structure of a self-compartmentalizing sulfur cycle metalloenzyme. Science. 2006 Feb 17;311(5763):996-1000.

Legend: The SOR holoenzyme. Cartoon representation viewed along the crystallographic fourfold axis. Note the protrusions at fourfold pseudo-symmetry axes.


Last Updated on Tuesday, 02 August 2011 19:08

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The Crystal Structure of the Human AAA+ Protein RuvBL1


The crystal structure of the molecular machine RuvBL1/RuvBL2 complex reveals a dodecamer consisting of two heterohexameric rings with alternating RuvBLl and RuvBL2 monomers bound to ADP/ATP. Our structural, biochemical and SAXS results give relevant insights into the assembly and illuminate the mechanism of how these proteins might exert their activities.


P. M. Matias, S. Gorynia, P. Donner, M. A. Carrondo, “Crystal Structure of the Human AAA+ Protein RuvBL1”, J. Biol. Chem. (2006) 281, 38918-38929

S. Gorynia, T. M. Bandeiras, F. G. Pinho, C. E. McVey, C. Vonrhein, A. Round, D. I. Svergun, P. Donner, P. M. Matias and M. A. Carrondo “Structural and functional insights into a dodecameric molecular machine – The RuvBL1/RuvBL2 complex”, submitted.

Legend:The crystal structure of RuvBL1 consists of hexamers, formed of ADP-bound monomers. The hexamers exhibit a central channel ca. 18 Å in diameter


Last Updated on Thursday, 26 March 2015 14:33

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The Structure of the Herpesvirus LANA Protein - Impact of LANA on Herpesvirus Latency


Herpesviruses establish life-long latent infections. During latency, gammaherpesviruses, such as Kaposi's sarcoma associated herpesvirus (KSHV), persist as multicopy, circularized genomes in the cell nucleus and express a small subset of viral genes. Latency-associated nuclear antigen (LANA) is the predominant gene expressed during latent infection. The X-ray structure determination of the Latency Associated Nuclear Antigen (LANA) has revealed the site of viral DNA tethering. This work elucidates the structure of the LANA DNA binding domain and identifies a novel surface feature that is critical for viral latent infection, likely by acting through a host cell protein.


Bruno Correia, Sofia A. Cerqueira, Chantal Beauchemin, Marta Pires de Miranda, Shijun Li, Rajesh Ponnusamy, Lénia Rodrigues, Thomas R. Schneider, Maria A. Carrondo, Kenneth M. Kaye, J. Pedro Simas and Colin E. McVey.
Crystal structure of the gamma-2 herpesvirus LANA DNA binding domain identifies charged surface residues which impact viral latency. PLoS Pathogens 2013 (online or pdf).


Last Updated on Friday, 27 March 2015 13:53

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 The membrane-bound complex cytochrome c nitrite reductase NrfHA


Figure 1

A novel family of cytochrome c quinol dehydrogenases, that play an important role in bacterial respiratory chains, was recognized in recent years. Here we describe the first structure of a member of this family, NrfH, from Desulfovibrio vulgaris, which forms a strong complex with its electron partner, the cytochrome c nitrite reductase NrfA.

The 2.3 Å crystal structure reveals that one NrfH molecule interacts with one NrfA dimer in an asymmetrical manner, forming a large membrane-bound complex with an overall a4b2 quaternary arrangement (Fig.1). NrfH is an a-helical protein with a novel protein fold (Fig.2a) which has a highly unusual heme coordination.

The menaquinol-interacting NrfH heme 1 is pentacoordinated, bound by a methionine from the CXXCHXM sequence (Met49), with an aspartate residue occupying the distal position (Fig.2b). The NrfH heme that transfers electrons to NrfA has a lysine residue from the closest NrfA molecule as distal ligand (Fig.2c). A likely menaquinol binding site, containing several conserved and essential residues, is identified.


Rodrigues, M.L., Oliveira, T., Pereira I.A.C., and Archer, M. (2006). The X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel heme coordination. EMBO J., in press.

Rodrigues, M.L., Oliveira, T., Matias, P.M., Martins, I.C., Valente, F.M.A., Pereira, I.A.C. and Archer, M. (2006). Crystallization and preliminary structure determination of the membrane-bound complex cytochrome c nitrite reductase from Desulfovibrio vulgaris Hildenborough. Acta Cryst. F62, 565-568.


Fig 1 (a) NrfHA viewed parallel to the membrane (gray rectangle) with hemes drawn as red sticks. Each NrfH subunit, shown in green and magenta, is tightly bound to one NrfA dimer shown in orange/yellow and light blue/dark blue. (b) Ensemble of 28 heme groups in the same orientation as in (a).

Fig 2 NrfH overall fold, where hemes are arranged in a di-heme parallel motif. The two longer a-helices are inserted in the membrane. (b) Menaquinol-interacting heme 1, with the proximal ligand, Met49, the His47 from the CXXCHXM motif and Asp89 displayed. (c) Heme 4, the gateway of electrons from NrfH to NrfA, has Lys331 from an internal NrfA subunit as distal heme ligand. The proximal ligand is His140 from NrfH.


Last Updated on Tuesday, 02 August 2011 20:02

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Macromolecular Crystallography Unit 2016

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