Developments in the<i>CCP</i>4 molecular-graphics project

Potterton, Liz; McNicholas, Stuart; Krissinel, Eugene; Gruber, Jan; Cowtan, Kevin; Emsley, Paul; Murshudov, Garib N.; Cohen, Serge; Perrakis, Anastassis; Noble, M.E.M.

doi:10.1107/s0907444904023716

Cited by 524 publications

(275 citation statements)

References 20 publications

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“…4) clearly indicates that the binding site for Cbl is broad and open on both sides of the molecule compared with TC. Upon binding to IF, the solvent accessibility area of Cbl is reduced to Ϸ19% compared with Ϸ7% in TC (23). This difference does not seem to influence the ability of Cbl to bind to these proteins, as shown by recent studies involving binding of fluorescent analogues and surface plasmon resonance, which show that the affinity of Cbl is similar for all three Cbl-binding proteins (25,26).…”

Section: Resultsmentioning

confidence: 56%

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Crystal structure of human intrinsic factor: Cobalamin complex at 2.6-Å resolution

Mathews¹,

Gordon

Chen³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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The structure of intrinsic factor (IF) in complex with cobalamin (Cbl) was determined at 2.6-Å resolution. The overall fold of the molecule is that of an ␣6/␣6 barrel. It is a two-domain protein, and the Cbl is bound at the interface of the domains in a base-on conformation. Surprisingly, two full-length molecules, each comprising an ␣-and a ␤-domain and one Cbl, and two truncated molecules with only an ␣-domain are present in the same asymmetric unit. The environment around Cbl is dominated by uncharged residues, and the sixth coordinate position of Co 2؉ is empty. A detailed comparison between the IF-B12 complex and another Cbl transport protein complex, trans-Cbl-B12, has been made. The pH effect on the binding of Cbl analogues in transport proteins is analyzed. A possible basis for the lack of interchangeability of human and rat IF receptors is presented.5] is a water-soluble vitamin and is essential for the growth and development of all mammals, including humans. Cbl is a member of the corrinoid series of cobalt-containing compounds and is distinguished from some other members of this group by possessing a nucleotide side chain terminating in dimethylbenzimidazole (1, 2). It serves as a key enzymatic cofactor for a number of methyltransferase and mutase reactions occurring in nature (3). In mammals, it contributes the prosthetic group for two important enzymes, methionine synthase (a methyltransferase) and methylmalonylCoA mutase (1, 2, 4).In mammals, three proteins are involved in the uptake, transport, and storage of Cbl. These are gastric intrinsic factor (IF), trans-Cbl II (TC), and haptocorrin (HC). These are immunologically distinct proteins with a protein core of Ϸ46 kDa. IF and HC are heavily glycosylated, but TC is not (5, 6). In humans, the genes for IF and HC are located in chromosome 22 (7,8), whereas the gene for TC is located in chromosome 11 (9). Human IF contains 399-aa residues plus Ϸ15% carbohydrate, giving it a molecular mass of Ϸ60 kDa, as observed by gel filtration (10-13). All three proteins promote Cbl entry through endocytosis involving distinct cell surface receptors (5,(14)(15)(16)(17)(18)(19)(20).Dietary Cbl is bound first to HC in the gastric lumen but is transferred to IF in the duodenum after degradation of HC by pancreatic proteases. IF is responsible for transit of Cbl through the small intestine and delivery of it to the endothelial cells that line the ileum. The IF-Cbl complex is then recognized by the IF-Cbl receptor, cubilin (CUB), located on the luminal side of the intestinal mucosal cells, and mediates its internalization. Lysosomal degradation of the internalized IF-Cbl complex releases Cbl, which is then able to bind to TC, probably within the enterocyte. The TC-Cbl complex is then translocated across the basolateral membrane and released into the circulation, to be taken up by TC-Cbl receptor-mediated process by all cells in the body. Lysosomal dissociation of the complex then occurs along with transfer of Cbl to the coenzyme methyl-and Ado-Cbl in the cytoplasm and i...

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Section: Resultsmentioning

confidence: 56%

“…Because the rmsd between bovine and human TC is only 1.2 Å, and the monoclinic form of bovine TC diffracted to higher resolution (2 Å) than did human TC (3.2 Å), a detailed Fig. 11) based on the secondary structure matching (22) carried out by using CCP4MG (23). Both TC and IF adopt an ␣ 6 -␣ 6 barrel motif.…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of human intrinsic factor: Cobalamin complex at 2.6-Å resolution

Mathews¹,

Gordon

Chen³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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“…Iterative cycles of refinement were carried out using the phenix-refine module within the Phenix program (37). Structural figures in this study were prepared using the CCP4MG program (38).…”

Section: Methodsmentioning

confidence: 99%

Characterization of a Novel WDR5-binding Site That Recruits RbBP5 through a Conserved Motif to Enhance Methylation of Histone H3 Lysine 4 by Mixed Lineage Leukemia Protein-1*

Odho¹,

Southall

Wilson

2010

Journal of Biological Chemistry

115

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Histone modification is well established as a fundamental mechanism driving the regulation of transcription, replication, and DNA repair through the control of chromatin structure. Likewise, it is apparent that incorrect targeting of histone modifications contributes to misregulated gene expression and hence to developmental disorders and diseases of genomic instability such as cancer. The KMT2 family of SET domain methyltransferases, typified by mixed lineage leukemia protein-1 (MLL1), is responsible for histone H3 lysine 4 methylation, a marker of active genes. To ensure that this modification is correctly targeted, a multiprotein complex associates with the methyltransferase and directs activity. We have identified a novel interaction site on the core complex protein WD repeat protein-5 (WDR5), and we mapped the complementary site on its partner retinoblastoma-binding protein-5 (RbBP5). We have characterized this interaction by x-ray crystallography and show how it is fundamental to the assembly of the complex and to the regulation of methyltransferase activity. We show which region of RbBP5 contributes directly to mixed lineage leukemia activation, and we combine our structural and biochemical data to produce a model to show how WDR5 and RbBP5 act cooperatively to stimulate activity.Aberrant regulation of epigenetic networks has been identified as a key driver of many diseases, especially where genomic instability is a factor, such as in developmentally related disorders and many cancers (1, 2). The principal signaling components of these networks are covalent post-translational modifications to the side chains of residues on the histone tails that extend beyond the nucleosome core (3). These modified residues generate specific binding sites for the chromatin-associated proteins and multiprotein complexes responsible for processes such as transcription, replication, and DNA repair and are thought to act in a highly coordinated fashion (4 -6). To create and maintain the correct gene transcription profiles and to facilitate the appropriate response to environmental stimulation, it is essential that the enzymes that deposit or remove these marks be accurately targeted and their activity tightly regulated. The best conserved modification is methylation of the histone H3 lysine 4 (H3K4) 3 residue that is predominantly, although not exclusively, associated with transcriptionally active genes (7,8). Lysine side chains can be mono, di-, or trimethylated, and it is essential that the correct level of H3K4 methylation be deposited on the appropriate nucleosomes, as it has been shown that the different levels of methylation are related with differing outcomes for the associated DNA (9). The Set1/MLL (KMT2) family of methyltransferases is the principal enzyme family responsible for H3K4 methylations, and an associated multiprotein complex has evolved to ensure that this activity is tightly regulated (10 -13).The KMT2 family of H3K4 methyltransferases include six members as follows: Set1A, Set1B, and the four mixed linea...

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“…We have implemented a finite-difference approach to this problem and made the resulting code available either as a stand-alone executable or as part of CCP4MG (Potterton et al, 2004). Our implementation exploits a rapid FFT-based algorithm to define the protein interior, 'anti-aliasing' to distribute charges within the initial potential map and optimal over-relaxation, based on the spectral radius of the PBE map, to speed up convergence of the finite difference approach.…”

Section: Electrostaticsmentioning

confidence: 99%

Computational analyses of the surface properties of protein–protein interfaces

Gruber

Zawaira

Saunders

et al. 2006

Acta Crystallogr D Biol Crystallogr

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Several potential applications of structural biology depend on discovering how one macromolecule might recognize a partner. Experiment remains the best way to answer this question, but computational tools can contribute where this fails. In such cases, structures may be studied to identify patches of exposed residues that have properties common to interaction surfaces and the locations of these patches can serve as the basis for further modelling or for further experimentation. To date, interaction surfaces have been proposed on the basis of unusual physical properties, unusual propensities for particular amino-acid types or an unusually high level of sequence conservation. Using the CXXSurface toolkit, developed as a part of the CCP4MG program, a suite of tools to analyse the properties of surfaces and their interfaces in complexes has been prepared and applied. These tools have enabled the rapid analysis of known complexes to evaluate the distribution of (i) hydrophobicity, (ii) electrostatic complementarity and (iii) sequence conservation in authentic complexes, so as to assess the extent to which these properties may be useful indicators of probable biological function.

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Developments in theCCP4 molecular-graphics project

Cited by 524 publications

References 20 publications

Crystal structure of human intrinsic factor: Cobalamin complex at 2.6-Å resolution

Crystal structure of human intrinsic factor: Cobalamin complex at 2.6-Å resolution

Characterization of a Novel WDR5-binding Site That Recruits RbBP5 through a Conserved Motif to Enhance Methylation of Histone H3 Lysine 4 by Mixed Lineage Leukemia Protein-1*

Computational analyses of the surface properties of protein–protein interfaces

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