CDD: a curated Entrez database of conserved domain alignments

Marchler‐Bauer, Aron; Anderson, John B.; DeWeese-Scott, Carol; Fedorova, Natalie D.; Geer, Lewis Y.; He, Siqian; Hurwitz, David I.; Jackson, John D.; Jacobs, Aviva R.; Lanczycki, Christopher J.; Liebert, Cynthia A.; Liu, Chunlei; Madej, Thomas; Marchler, Gabriele H.; Mazumder, Raja; Nikol'skaya, A. N.; Panchenko, Anna R.; Rao, Bachoti S.; Shoemaker, Benjamin A.; Simonyan, Vahan; Song, Jakyoung; Thiessen, Paul A.; Vasudevan, Sona; Wang, Yanli; Yamashita, Roxanne A.; Yin, Jodie J.; Bryant, Stephen H.

doi:10.1093/nar/gkg087

Cited by 696 publications

(496 citation statements)

References 12 publications

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“…This result was supported by a conserved domain search (38) at NCBI using RPS-BLAST, which produced a significant alignment (E value, 2e-42) of LamA with the acetamidase/formamidase family of proteins as defined by the Pfam database (FmdA_AmdA; accession no. PF03069).…”

Section: Resultsmentioning

confidence: 72%

l-Selective Amidase with Extremely Broad Substrate Specificity fromOchrobactrum anthropiNCIMB 40321

Sonke¹,

Ernste²,

Tandler³

et al. 2005

Appl Environ Microbiol

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An industrially attractive L-specific amidase was purified to homogeneity from Ochrobactrum anthropi NCIMB 40321 wild-type cells. The purified amidase displayed maximum initial activity between pH 6 and 8.5 and was fully stable for at least 1 h up to 60°C. The purified enzyme was strongly inhibited by the metal-chelating compounds EDTA and 1,10-phenanthroline. The activity of the EDTA-treated enzyme could be restored by the addition of Zn 2؉ (to 80%), Mn 2؉ (to 400%), and Mg 2؉ (to 560%). Serine and cysteine protease inhibitors did not influence the purified amidase. This enzyme displayed activity toward a broad range of substrates consisting of ␣-hydrogen-and (bulky) ␣,␣-disubstituted ␣-amino acid amides, ␣-hydroxy acid amides, and ␣-N-hydroxyamino acid amides. In all cases, only the L-enantiomer was hydrolyzed, resulting in E values of more than 150. Simple aliphatic amides, ␤-amino and ␤-hydroxy acid amides, and dipeptides were not converted. The gene encoding this L-amidase was cloned via reverse genetics. It encodes a polypeptide of 314 amino acids with a calculated molecular weight of 33,870. Since the native enzyme has a molecular mass of about 66 kDa, it most likely has a homodimeric structure. The deduced amino acid sequence showed homology to a few other stereoselective amidases and the acetamidase/ formamidase family of proteins (Pfam FmdA_AmdA). Subcloning of the gene in expression vector pTrc99A enabled efficient heterologous expression in Escherichia coli. Altogether, this amidase has a unique set of properties for application in the fine-chemicals industry.Enantiomerically pure ␣-amino acids, both natural and unnatural, form an important class of chiral building blocks for the pharmaceutical and agrochemical industries. Examples of important ␣-hydrogen-␣-amino acids are D-phenylglycine (DPhg) and D-p-hydroxyphenylglycine, which are produced as side chains for the manufacture of semisynthetic ␤-lactam antibiotics such as ampicillin, amoxicillin, and cephalexin (14, 53), and D-valine, an intermediate for the pyrethroid insecticide fluvalinate (28). Another frequently used ␣-hydrogen-␣-amino acid is L-tert-leucine, which is used as a building block for a variety of antiviral (e.g., anti-human immunodeficiency virus), antiarthritis, and anticancer drugs under development and as a chiral auxiliary in chemical asymmetric synthesis (5, 10). Besides ␣-hydrogen-␣-amino acids, ␣,␣-disubstituted ␣-amino acids also constitute a group of compounds of increasing importance, as exemplified by the use of L-␣-methyl-3,4-dihydroxyphenylalanine (L-␣-methyldopa) as an antihypertensive drug (34, 42), ␣-methylvaline as an intermediate for the herbicide Arsenal and related herbicides (47, 49), and L-␣-methylphenylglycine as a building block for the new fungicide fenamidone (27).Enantiomerically pure ␣-amino acids can be produced on a commercial scale by a number of different processes, both chemical and enzymatic. Biocatalytic processes that have been commercialized include the acylase process operated by Degussa (8) a...

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Section: Resultsmentioning

confidence: 72%

l-Selective Amidase with Extremely Broad Substrate Specificity fromOchrobactrum anthropiNCIMB 40321

Sonke¹,

Ernste²,

Tandler³

et al. 2005

Appl Environ Microbiol

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“…The vWFA motif is a structural fold that is present in a wide range of proteins that mediate protein-protein interactions (for review, see Whittaker and Hynes, 2002), including both ␤ and ␣ integrins, and this motif is also commonly referred to as a ␤-integrin motif. Analysis of the Conserved Domain Database at National Center for Biotechnology Information (Marchler-Bauer et al, 2003) demonstrates these motifs as closely related. ClustalW sequence alignments further demonstrate the similarity of this segment of VwkA to both integrins and vWFA family members ( Figure 1A).…”

Section: Identification and Cloning Of A Novel ␣-Kinase Cdnamentioning

confidence: 99%

Identification and Characterization of a Novel α-Kinase with a von Willebrand Factor A-like Motif Localized to the Contractile Vacuole and Golgi Complex inDictyostelium discoideum

Betapudi

Mason

Licate

et al. 2005

MBoC

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We have identified a new protein kinase in Dictyostelium discoideum that carries the same conserved class of "␣-kinase" catalytic domain as reported previously in myosin heavy chain kinases (MHCKs) in this amoeba but that has a completely novel domain organization. The protein contains an N-terminal von Willebrand factor A (vWFA)-like motif and is therefore named VwkA. Manipulation of VwkA expression level via high copy number plasmids (VwkA ؉؉ cells) or gene disruption (vwkA null cells) results in an array of cellular defects, including impaired growth and multinucleation in suspension culture, impaired development, and alterations in myosin II abundance and assembly. Despite sequence similarity to MHCKs, the purified protein failed to phosphorylate myosin II in vitro. Autophosphorylation activity, however, was enhanced by calcium/calmodulin, and the enzyme can be precipitated from cellular lysates with calmodulin-agarose, suggesting that VwkA may directly bind calmodulin. VwkA is cytosolic in distribution but enriched on the membranes of the contractile vacuole and Golgi-like structures in the cell. We propose that VwkA likely acts indirectly to influence myosin II abundance and assembly behavior and possibly has broader roles than previously characterized ␣ kinases in this organism, which all seem to be MHCKs. INTRODUCTIONNearly all aspects of cell life are regulated by protein phosphorylation involving a large number of biochemical reactions and distinct signaling pathways. Existence of ϳ500 genes encoding various protein kinases in the human genome further underscores their importance in cell life (Manning et al., 2002). Most of these conventional protein kinases belong to serine/threonine/tyrosine, a kinase superfamily whose members carry a conserved catalytic domain with recognizable sequence similarity in spite of having different targets in the cell (Hardie, 1994;Hanks and Hunter, 1995). In recent years, however, biochemical and molecular approaches have led to the identification of more divergent classes of eukaryotic protein kinases carrying a catalytic domain sequence with no sequence similarity with conventional protein kinase catalytic domains (Manning et al., 2002). One major class of unconventional protein kinases was first identified via representatives of myosin heavy chain kinases (MHCKs) in Dictyostelium discoideum (Futey et al., 1995;Côté et al., 1997) and via identification of mammalian eEF-2 kinase (eEF-2K) as an unconventional protein kinase (Ryazanov et al., 1997). This novel, conserved group of unconventional eukaryotic protein kinases has been termed the ␣-kinase family (Ryazanov et al., 1999;Drennan and Ryazanov, 2004).Molecular cloning and biochemical characterization studies demonstrated that at least three Dictyostelium ␣-kinases genes encode enzymes that can specifically phosphorylate myosin II heavy chain (MHC) in vitro and in vivo, and were thus named as MHC kinase A (MHCK A), MHC kinase B (MHCK B) and MHC kinase C (MHCK C) (Futey et al., 1995;Clancy et al., 1997;Luo et al., 200...

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“…nlm.nih.gov/Structure/cdd/cdd.shtml) (20) (29) and the Hybrigenics PIMRider (30). Putative promoter regions of the studied H.in¯uenzae genes were compared with upstream regions of all H.in¯uenzae and E.coli genes using the OWEN program (31).…”

Section: Functional Characterization Of Genesmentioning

confidence: 99%

Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae

Kolker¹,

Makarova

Shabalina

et al. 2004

Nucleic Acids Research

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The progress in genome sequencing has led to a rapid accumulation in GenBank submissions of uncharacterized`hypothetical' genes. These genes, which have not been experimentally characterized and whose functions cannot be deduced from simple sequence comparisons alone, now comprise a signi®cant fraction of the public databases. Expression analyses of Haemophilus in¯uenzae cells using a combination of transcriptomic and proteomic approaches resulted in con®dent identi®ca-tion of 54`hypothetical' genes that were expressed in cells under normal growth conditions. In an attempt to understand the functions of these proteins, we used a variety of publicly available analysis tools. Close homologs in other species were detected for each of the 54`hypothetical' genes. For 16 of them, exact functional assignments could be found in one or more public databases. Additionally, we were able to suggest general functional characterization for 27 more genes (comprising~80% total). Findings from this analysis include the identi®cation of a pyruvate-formate lyase-like operon, likely to be expressed not only in H.in¯uenzae but also in several other bacteria. Further, we also observed three genes that are likely to participate in the transport and/or metabolism of sialic acid, an important component of the H.in¯uenzae lipo-oligosaccharide. Accurate functional annotation of uncharacterized genes calls for an integrative approach, combining expression studies with extensive computational analysis and curation, followed by eventual experimental veri®cation of the computational predictions.

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CDD: a curated Entrez database of conserved domain alignments

Cited by 696 publications

References 12 publications

l-Selective Amidase with Extremely Broad Substrate Specificity fromOchrobactrum anthropiNCIMB 40321

l-Selective Amidase with Extremely Broad Substrate Specificity fromOchrobactrum anthropiNCIMB 40321

Identification and Characterization of a Novel α-Kinase with a von Willebrand Factor A-like Motif Localized to the Contractile Vacuole and Golgi Complex inDictyostelium discoideum

Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae

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