The <i>Methanocaldococcus jannaschii</i> protein Mj0968 is not a P‐type ATPase

Bramkamp, Marc; Gaßel, Michael; Herkenhoff-Hesselmann, Brigitte; Bertrand, Jessica; Altendorf, Karlheinz

doi:10.1016/s0014-5793(03)00372-7

Cited by 3 publications

(3 citation statements)

References 24 publications

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“…Phosphatase ActiVity. The phosphatase activity of the purified H4H5 loop was measured using a microtiter assay as previously described (24). The total reaction volume was 100 µL containing 20 mM HEPES/Tris, pH 7.8, 15 mM MgCl 2 , and 50 µg mL -1 protein.…”

Section: Methodsmentioning

confidence: 99%

Functional Modules of KdpB, the Catalytic Subunit of the Kdp-ATPase from Escherichia coli

Bramkamp

Altendorf

2004

Biochemistry

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The large cytoplasmic domain (H4H5) of KdpB of the KdpFABC complex (P-type ATPase) from Escherichia coli consists of two separate modules, the phosphorylation domain (KdpBP) and the nucleotide binding domain (KdpBN). The H4H5 and the KdpBN domains were purified as soluble 10His-tagged fusion proteins. Both proteins exhibit a mainly alpha-helical secondary structure as judged by CD spectroscopy. Fluorescein 5-isothiocyanate (FITC) labeling studies revealed that both proteins form a proper nucleotide binding site. Adenosine nucleotides protect the H4H5 loop but not KdpBN against FITC modification. Trinitrophenyl (TNP)-nucleotide binding studies revealed that both H4H5 and KdpBN bind nucleotides with high affinity. Furthermore, the H4H5 loop was still able to hydrolyze ATP, as well as p-nitrophenyl phosphate (pNPP). These results lend support to the notion that the separately synthesized H4H5 and KdpBN domains retain their native structure and that they reveal properties of both P2-type ATPases (e.g., Na(+),K(+)-ATPase and Ca(2+)-ATPase) and P1b-type ATPases (e.g., heavy metal transporting ATPases). Furthermore, this report also emphasizes the unique position of the Kdp-ATPase within the P-type ATPase family.

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Section: Methodsmentioning

confidence: 99%

Functional Modules of KdpB, the Catalytic Subunit of the Kdp-ATPase from Escherichia coli

Bramkamp

Altendorf

2004

Biochemistry

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“…162 A small subfamily related to the P-type ATPases found only in euryarchaeota and lacking transmembrane regions and the conserved lysine and threonine residues of this family was recently studied experimentally 163 and proposed to be a phosphatase. 164 We propose naming this group of proteins the type VI P-type ATPase subfamily as their structure and sequence features suggest that they are the only surviving form close to the precursor of all other P-type ATPases.…”

Section: The P-type Atpase Familymentioning

confidence: 99%

Evolutionary Genomics of the HAD Superfamily: Understanding the Structural Adaptations and Catalytic Diversity in a Superfamily of Phosphoesterases and Allied Enzymes

Burroughs¹,

Allen²,

Dunaway‐Mariano³

et al. 2006

Journal of Molecular Biology

387

520

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The HAD (haloacid dehalogenase) superfamily includes phosphoesterases, ATPases, phosphonatases, dehalogenases, and sugar phosphomutases acting on a remarkably diverse set of substrates. The availability of numerous crystal structures of representatives belonging to diverse branches of the HAD superfamily provides us with a unique opportunity to reconstruct their evolutionary history and uncover the principal determinants that led to their diversification of structure and function. To this end we present a comprehensive analysis of the HAD superfamily that identifies their unique structural features and provides a detailed classification of the entire superfamily. We show that at the highest level the HAD superfamily is unified with several other superfamilies, namely the DHH, receiver (CheY-like), von Willebrand A, TOPRIM, classical histone deacetylases and PIN/FLAP nuclease domains, all of which contain a specific form of the Rossmannoid fold. These Rossmannoid folds are distinguished from others by the presence of equivalently placed acidic catalytic residues, including one at the end of the first core β-strand of the central sheet. The HAD domain is distinguished from these related Rossmannoid folds by two key structural signatures, a "squiggle" (a single helical turn) and a "flap" (a beta hairpin motif) located immediately downstream of the first β-strand of their core Rossmanoid fold. The squiggle and the flap motifs are predicted to provide the necessary mobility to these enzymes for them to alternate between the "open" and "closed" conformations. In addition, most members of the HAD superfamily contains inserts, termed caps, occurring at either of two positions in the core Rossmannoid fold. We show that the cap modules have been independently inserted into these two stereotypic positions on multiple occasions in evolution and display extensive evolutionary diversification independent of the core catalytic domain. The first group of caps, the C1 caps, is directly inserted into the flap motif and regulates access of reactants to the active site. The second group, the C2 caps, forms a roof over the active site, and access to their internal cavities might be in part regulated by the movement of the flap. The diversification of the cap module was a major factor in the exploration of a vast substrate space in the course of the evolution of this superfamily. We show that the HAD superfamily contains 33 major families distributed across the three superkingdoms of life. Analysis of the phyletic patterns suggests that at least five distinct HAD proteins are traceable to the last universal common ancestor (LUCA) of all extant organisms. While these prototypes diverged prior to the emergence Abbreviations used: HAD, haloacid dehalogenase; PNKP, polynucleotide kinase phosphatase; KDO 8-P, deoxy-Dmannose-octulosonate 8-phosphate; CTD, carboxyl-terminal domain; PNKP, polynucleotide kinase phosphatase; LUCA, last universal common ancestor.E-mail address of the corresponding author: aravind@ncbi.nlm.nih.gov of the LUCA, t...

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“…The specificity and annotation depth of predicted partners for COGs/NOGs of unknown function varies. Associated partners range from well-defined and experimentally characterized COGs, when, for instance, the hypothetical COG3310 phylogenetically co-occurs significantly in several proteobacteria with an experimentally characterized operon of pilus assembly proteins (18), to barely specified pathways such as COG4029, COG4048, COG4050, COG4051, COG4052 and COG4069, which appear only in methanogenic archaea in a conserved operon with genes coding for phosphatases (COG4087) (19,20) (Table 1).…”

Section: Resultsmentioning

confidence: 99%

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes

Doerks

Mering

Bork

2004

Nucleic Acids Research

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Three integrated genomic context methods were used to annotate uncharacterized proteins in 102 bacterial genomes. Of 7853 orthologous groups with unknown function containing 45,110 proteins, 1738 groups could be linked to functionally associated partners. In many cases, those partners are uncharacterized themselves (hinting at newly identified modules) or have been described in general terms only. However, we were able to assign pathways, cellular processes or physical complexes for 273 groups (encompassing 3624 previously functionally uncharacterized proteins).

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The Methanocaldococcus jannaschii protein Mj0968 is not a P‐type ATPase

Cited by 3 publications

References 24 publications

Functional Modules of KdpB, the Catalytic Subunit of the Kdp-ATPase from Escherichia coli

Functional Modules of KdpB, the Catalytic Subunit of the Kdp-ATPase from Escherichia coli

Evolutionary Genomics of the HAD Superfamily: Understanding the Structural Adaptations and Catalytic Diversity in a Superfamily of Phosphoesterases and Allied Enzymes

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes

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