Structure of creatine amidinohydrolase from Actinobacillus

Padmanabhan, Balasundaram; Paehler, A.; Horikoshi, Masami

doi:10.1107/s0907444902010156

Cited by 7 publications

(8 citation statements)

References 22 publications

(29 reference statements)

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“…1). This architecture is also found in the aminopeptidases that share limited sequence similarity with the Spt16 NTD, including methionine aminopeptidase, prolidase, and aminopeptidase P. Other structurally similar proteins include creatinase (39,40) and the ErbB-3 receptor-binding protein (Ebp1; 41,42). The C-terminal lobe shows closest structural similarity to the prolidase enzyme from Pyrococcus furiosus (PDB 1PV9; 43), which overlaps with a root mean square deviation of 2.0 Å over 215 pairs of C-␣ atoms that share 23% sequence identity (Fig.…”

Section: Resultsmentioning

confidence: 97%

Structural and Functional Analysis of the Spt16p N-terminal Domain Reveals Overlapping Roles of yFACT Subunits

VanDemark

Hua

McCullough

et al. 2008

Journal of Biological Chemistry

114

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yFACT (heterodimers of Saccharomyces cerevisiae Spt16-Pob3 combined with Nhp6) binds to and alters the properties of nucleosomes. The essential function of yFACT is not disrupted by deletion of the N-terminal domain (NTD) of Spt16 or by mutation of the middle domain of Pob3, but either alteration makes yeast cells sensitive to DNA replication stress. We have determined the structure of the Spt16 NTD and find evidence for a conserved potential peptide-binding site. Pob3-M also contains a putative binding site, and we show that these two sites perform an overlapping essential function. We find that yFACT can bind the N-terminal tails of some histones and that this interaction is important for yFACT-nucleosome binding. However, neither the Spt16 NTD nor a key residue in the putative Pob3-M-binding site was required for interactions with histone N termini or for yFACT-mediated nucleosome reorganization in vitro. Instead, both potential binding sites interact functionally with the C-terminal docking domain of the histone H2A. yFACT therefore appears to make multiple contacts with different sites within nucleosomes, and these interactions are partially redundant with one another. The docking domain of H2A is identified as an important participant in maintaining stability during yFACT-mediated nucleosome reorganization, suggesting new models for the mechanism of this activity.yFACT (yeast facilitator of chromatin transcription or transactions) is a heterodimer of the Saccharomyces cerevisiae Spt16 and Pob3 proteins that is assisted in vivo and in vitro by the high mobility group type B domain DNA-binding protein Nhp6 (1, 2). In vitro, yFACT binds to histones (3, 4) and can alter the accessibility of DNA within nucleosomes without hydrolyzing ATP and without repositioning the histone octamer core relative to the DNA (5-7). This activity is different from ATP-dependent chromatin remodeling and has been called nucleosome reorganization (6). yFACT and related FACT complexes from other eukaryotes are needed for both normal regulation of transcription (5, 8 -11) and for DNA replication (12-20). Reorganization activity therefore appears to be important in a range of chromatin-based processes, including initiation and elongation of transcription, establishment and maintenance of normal chromatin, and survival during DNA replication stress. Consistent with this broad functional importance, FACT family members have been found in all eukaryotes examined, and at least one of the subunits is essential for viability in all cases reported (9,21,19,22).FACT complexes contain several distinct structural domains (16, 23), but little is known about how these domains contribute to FACT function. The middle domain of Pob3 (Pob3-M) forms two pleckstrin homology (PH) 4 folds that are closely juxtaposed (23), with highly conserved surface residues forming a patch in a region often associated with binding sites in PH domain proteins (23). Altering this patch caused increased sensitivity to hydroxyurea (HU) (23), a toxin that blocks dNTP synt...

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Section: Resultsmentioning

confidence: 97%

Structural and Functional Analysis of the Spt16p N-terminal Domain Reveals Overlapping Roles of yFACT Subunits

VanDemark

Hua

McCullough

et al. 2008

Journal of Biological Chemistry

114

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“…Creatinase has been found in Alcaligenes [15], Actinobacillus [16], Arthrobacter [17], Flavobacterium [18], Bacillus [19,20], Candidatus [21], Paracoccus [22] and Pseudomaonas [9,23,24], etc. There was no report about these strains that may live in the medium without organic source except for creatinine.…”

Section: Discussionmentioning

confidence: 99%

Biochemical and molecular characterization of a novel high activity creatine amidinohydrolase from Arthrobacter nicotianae strain 02181

Zhi

Kong

Zang

et al. 2009

Process Biochemistry

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“…Other M24B family members, such as creatinase from Actinobacillus, are known to be dimeric (Padmanabhan et al, 2002). To determine the association state of DddP, the purified protein was analysed by sedimentation equilibrium analytical ultracentrifugation.…”

Section: Purification Of Dimeric Dddp Enzymementioning

confidence: 99%

The dddP gene of Roseovarius nubinhibens encodes a novel lyase that cleaves dimethylsulfoniopropionate into acrylate plus dimethyl sulfide

et al. 2010

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The cloned dddP gene of the marine bacterium Roseovarius nubinhibens allows Escherichia coli to form the volatile dimethyl sulfide (DMS) from dimethylsulfoniopropionate (DMSP), an abundant anti-stress compatible solute made by many marine plankton and macroalgae. Using purified DddP, we show here that this enzyme is a DMSP lyase that cleaves DMSP to DMS plus acrylate. DddP forms a functional homodimeric enzyme, has a pH optimum of 6.0 and was a K m of~14 mM for the DMSP substrate. DddP belongs to the M24B family of peptidases, some members of which have metal cofactors. However, the metal chelators EDTA and bipyridyl did not affect DddP activity in vitro and the as-isolated enzyme did not contain metal ions. Thus, DddP resembles those members of the M24B family, such as creatinase, which also act on a non-peptide substrate and have no metal cofactor. Site-directed mutagenesis of the active-site region of DddP completely abolished its activity. Another enzyme, termed DddL, which occurs in other alphaproteobacteria, had also been shown to generate DMS plus acrylate from DMSP. However, DddL and DddP have no sequence similarity to each other, so DddP represents a second, wholly different class of DMSP lyase.

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Structure of creatine amidinohydrolase from Actinobacillus

Cited by 7 publications

References 22 publications

Structural and Functional Analysis of the Spt16p N-terminal Domain Reveals Overlapping Roles of yFACT Subunits

Structural and Functional Analysis of the Spt16p N-terminal Domain Reveals Overlapping Roles of yFACT Subunits

Biochemical and molecular characterization of a novel high activity creatine amidinohydrolase from Arthrobacter nicotianae strain 02181

The dddP gene of Roseovarius nubinhibens encodes a novel lyase that cleaves dimethylsulfoniopropionate into acrylate plus dimethyl sulfide

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