Biomedical subjects

Dachuan Zhang

Publications and source records attributed to Dachuan Zhang.

4 recordsLinked to original sources

PubMed2006

CDD: a conserved domain database for interactive domain family analysis.

The conserved domain database (CDD) is part of NCBI's Entrez database system and serves as a primary resource for the annotation of conserved domain footprints on protein sequences in Entrez. Entrez's global query interface can be accessed at http://www.ncbi.nlm.nih.gov/Entrez and will search CDD and many other databases. Domain annotation for proteins in Entrez has been pre-computed and is readily available in the form of 'Conserved Domain' links. Novel protein sequences can be scanned against CDD using the CD-Search service; this service searches databases of CDD-derived profile models with protein sequence queries using BLAST heuristics, at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. Protein query sequences submitted to NCBI's protein BLAST search service are scanned for conserved domain signatures by default. The CDD collection contains models imported from Pfam, SMART and COG, as well as domain models curated at NCBI. NCBI curated models are organized into hierarchies of domains related by common descent. Here we report on the status of the curation effort and present a novel helper application, CDTree, which enables users of the CDD resource to examine curated hierarchies. More importantly, CDD and CDTree used in concert, serve as a powerful tool in protein classification, as they allow users to analyze protein sequences in the context of domain family hierarchies.

Amino Acid Sequence↗

PubMed2005

CDD: a Conserved Domain Database for protein classification.

The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein-protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system.

Amino Acid Sequence↗

PubMed2002

Determination of the structure of an endoglucanase from Aspergillus niger and its mode of inhibition by palladium chloride.

The fungus Aspergillus niger is a main source of industrial cellulase. beta-1,4-Endoglucanase is the major component of cellulase from A. niger. In spite of widespread applications, little is known about the structure of this enzyme. Here, the structure of beta-1,4-endoglucanase from A. niger (EglA) was determined at 2.1 A resolution. Although there is a low sequence identity between EglA and CelB2, another member of family 12, the three-dimensional structures of their core regions are quite similar. The structural differences are mostly found in the loop regions, where CelB2 has an extra beta-sheet (beta-sheet C) at the non-reducing end of the binding cleft of the native enzyme. Incubation of EglA with PdCl(2) irreversibly inhibits the EglA activity. Structural studies of the enzyme-palladium complex show that three Pd(2+) ions bind to each EglA molecule. One of the Pd(2+) ions forms a coordinate covalent bond with Met118 S(delta) and the nucleophilic Glu116 O(epsilon1) at the active site of the enzyme. The other two Pd(2+) ions bind on the surface of the protein. Binding of Pd(2+) ions to EglA does not change the general conformation of the backbone of the protein significantly. Based on this structural study, one can conclude that the palladium ion directly binds to and blocks the active site of EglA and thus inactivates the enzyme.

Amino Acid Sequence↗

PubMed2002

Membrane association and kinase-like motifs of the RamC protein of Streptomyces coelicolor.

The protein RamC is required for the production of the spore-forming cells called aerial hyphae by the filamentous bacterium Streptomyces coelicolor. We showed that RamC, which contains several weakly predicted membrane-spanning sequences, is located exclusively in the S. coelicolor membrane. By constructing site-directed mutants in the cloned ramC gene and complementing a ramC null mutant, we showed that protein kinase-like sequence motifs in the amino-terminal half of the protein are required for function in vivo. These data suggest that RamC is a membrane-associated receptor kinase.

Amino Acid Motifs↗