Cloning and Sequencing of a Form II Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase from the Bacterial Symbiont of the Hydrothermal Vent Tubeworm Riftia pachyptila

ABSTRACT The bacterial symbiont of the hydrothermal vent tubeworm fixes carbon via the Calvin-Benson cycle and has been shown previously to express a form II ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). The gene cbbM, which encodes this enzyme, has been cloned and sequenced. The gene has the highest identity with thecbbM gene from Rhodospirillum rubrum, and analysis of the inferred amino acid sequence reveals that all active-site residues are conserved. This is the first form II RubisCO cloned and sequenced from a chemoautotrophic symbiont and from a deep-sea organism.

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Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis

eLife ◽

10.7554/elife.58371 ◽

2021 ◽

Vol 10 ◽

Author(s):

Tjorven Hinzke ◽

Manuel Kleiner ◽

Mareike Meister ◽

Rabea Schlüter ◽

Christian Hentschker ◽

...

Keyword(s):

Deep Sea ◽

Hydrothermal Vent ◽

Carbon Fixation ◽

Density Gradient Centrifugation ◽

Gradient Centrifugation ◽

Bacterial Symbiont ◽

Riftia Pachyptila ◽

Physiological Diversity ◽

Host Interaction ◽

Sulfur Oxidizing

The hydrothermal vent tubeworm Riftia pachyptila hosts a single 16S rRNA phylotype of intracellular sulfur-oxidizing symbionts, which vary considerably in cell morphology and exhibit a remarkable degree of physiological diversity and redundancy, even in the same host. To elucidate whether multiple metabolic routes are employed in the same cells or rather in distinct symbiont subpopulations, we enriched symbionts according to cell size by density gradient centrifugation. Metaproteomic analysis, microscopy, and flow cytometry strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: While small symbionts actively divide and may establish cellular symbiont-host interaction, large symbionts apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Moreover, in large symbionts, carbon fixation and biomass production seem to be metabolic priorities. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.

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Derived amino acid sequence and identification of active site residues of Escherichia coli beta-hydroxydecanoyl thioester dehydrase.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)68830-1 ◽

1988 ◽

Vol 263 (10) ◽

pp. 4641-4646 ◽

Cited By ~ 3

Author(s):

J E Cronan ◽

W B Li ◽

R Coleman ◽

M Narasimhan ◽

D de Mendoza ◽

...

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Amino Acid Sequence ◽

Active Site ◽

Active Site Residues

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Novel 4,6-Disubstituted s-Triazin-2-yl Amino Acid Derivatives as Promising Antifungal Agents

Journal of Fungi ◽

10.3390/jof6040237 ◽

2020 ◽

Vol 6 (4) ◽

pp. 237

Author(s):

Rakia Abd Alhameed ◽

Zainab Almarhoon ◽

Essam N. Sholkamy ◽

Salman Ali Khan ◽

Zaheer Ul-Haq ◽

...

Keyword(s):

Amino Acid ◽

Antifungal Activity ◽

Active Site ◽

Antifungal Agents ◽

Docking Studies ◽

Amino Acid Derivatives ◽

Active Site Residues ◽

Standard Drug ◽

Drug Compounds ◽

Inhibition Zones

A novel series of 4,6-disubstituted s-triazin-2-yl amino acid derivatives was prepared and characterized. Most of them showed antifungal activity against Candida albicans compared to clotrimazole (standard drug). Compounds bearing aniline derivatives, piperidine and glycine on the triazine core showed the highest inhibition zones at concentrations of 50, 100, 200, and 300 μg per disc. In addition, docking studies revealed that all the compounds accommodated well in the active site residues of N-myristoltransferase (NMT) and exhibited complementarity, which explains the observed antifungal activity. Interestingly, none of these compounds showed antibacterial activity.

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Development and characterization of 12 microsatellite markers from the deep-sea hydrothermal vent siboglinid Riftia pachyptila

Molecular Ecology Resources ◽

10.1111/j.1471-8286.2007.01897.x ◽

2008 ◽

Vol 8 (1) ◽

pp. 132-134 ◽

Cited By ~ 7

Author(s):

A. J. FUSARO ◽

A. R. BACO ◽

G. GERLACH ◽

T. M. SHANK

Keyword(s):

Microsatellite Markers ◽

Deep Sea ◽

Hydrothermal Vent ◽

Riftia Pachyptila

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Modification of Rhodospirillum rubrum ribulose bisphosphate carboxylase with pyridoxal phosphate. 1. Identification of a lysyl residue at the active site

Biochemistry ◽

10.1021/bi00600a023 ◽

1978 ◽

Vol 17 (7) ◽

pp. 1282-1287 ◽

Cited By ~ 34

Author(s):

William B. Whitman ◽

F. Robert Tabita

Keyword(s):

Active Site ◽

Pyridoxal Phosphate ◽

Rhodospirillum Rubrum ◽

Ribulose Bisphosphate Carboxylase ◽

Ribulose Bisphosphate ◽

Bisphosphate Carboxylase ◽

Lysyl Residue

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The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme

Molecules ◽

10.3390/molecules26165053 ◽

2021 ◽

Vol 26 (16) ◽

pp. 5053

Author(s):

Alina K. Bakunova ◽

Alena Yu. Nikolaeva ◽

Tatiana V. Rakitina ◽

Tatiana Y. Isaikina ◽

Maria G. Khrenova ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Structural Analysis ◽

Active Site ◽

Active Sites ◽

Structural Basis ◽

Active Site Residues ◽

Type Iv ◽

Fold Type ◽

Arginine Residues

Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.

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PREMONITION - Preprocessing motifs in protein structures for search acceleration

F1000Research ◽

10.12688/f1000research.5166.1 ◽

2014 ◽

Vol 3 ◽

pp. 217 ◽

Cited By ~ 3

Author(s):

Sandeep Chakraborty ◽

Basuthkar J. Rao ◽

Bjarni Asgeirsson ◽

Ravindra Venkatramani ◽

Abhaya M. Dandekar

Keyword(s):

Protein Structure ◽

Amino Acid ◽

Active Site ◽

Active Sites ◽

Protein Structures ◽

3D Structure ◽

Search Space ◽

Computational Method ◽

Computational Time ◽

Active Site Residues

The remarkable diversity in biological systems is rooted in the ability of the twenty naturally occurring amino acids to perform multifarious catalytic functions by creating unique structural scaffolds known as the active site. Finding such structrual motifs within the protein structure is a key aspect of many computational methods. The algorithm for obtaining combinations of motifs of a certain length, although polynomial in complexity, runs in non-trivial computer time. Also, the search space expands considerably if stereochemically equivalent residues are allowed to replace an amino acid in the motif. In the present work, we propose a method to precompile all possible motifs comprising of a set (n=4 in this case) of predefined amino acid residues from a protein structure that occur within a specified distance (R) of each other (PREMONITION). PREMONITION rolls a sphere of radius R along the protein fold centered at the C atom of each residue, and all possible motifs are extracted within this sphere. The number of residues that can occur within a sphere centered around a residue is bounded by physical constraints, thus setting an upper limit on the processing times. After such a pre-compilation step, the computational time required for querying a protein structure with multiple motifs is considerably reduced. Previously, we had proposed a computational method to estimate the promiscuity of proteins with known active site residues and 3D structure using a database of known active sites in proteins (CSA) by querying each protein with the active site motif of every other residue. The runtimes for such a comparison is reduced from days to hours using the PREMONITION methodology.

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Comparative Characterization of CTX-M-64 and CTX-M-14 Provides Insights into the Structure and Catalytic Activity of the CTX-M Class of Enzymes

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00917-16 ◽

2016 ◽

Vol 60 (10) ◽

pp. 6084-6090 ◽

Cited By ~ 8

Author(s):

Dandan He ◽

Jiachi Chiou ◽

Zhenling Zeng ◽

Edward Wai-Chi Chan ◽

Jian-Hua Liu ◽

...

Keyword(s):

Catalytic Activity ◽

Amino Acid ◽

Active Site ◽

Structural Integrity ◽

Amino Acid Residues ◽

Active Site Residues ◽

Significant Difference ◽

Function Relationship ◽

Alignment Analysis ◽

M 14

ABSTRACTClinical isolates producing hybrid CTX-M β-lactamases, presumably due to recombination between theblaCTX-M-15andblaCTX-M-14elements, have emerged in recent years. Among the hybrid enzymes, CTX-M-64 and CTX-M-14 display the most significant difference in catalytic activity. This study aims to investigate the mechanisms underlying such differential enzymatic activities in order to provide insight into the structure/function relationship of this class of enzymes. Sequence alignment analysis showed that the major differences between the amino acid composition of CTX-M-64 and CTX-M-14 lie at both the N and C termini of the enzymes. Single or multiple amino acid substitutions introduced into CTX-M-64 and CTX-M-14 were found to produce only minor effects on hydrolytic functions; such a finding is consistent with the notion that the discrepancy between the functional activities of the two enzymes is not the result of only a few amino acid changes but is attributable to interactions between a unique set of amino acid residues in each enzyme. This theory is supported by the results of the thermal stability assay, which confirmed that CTX-M-64 is significantly more stable than CTX-M-14. Our data confirmed that, in addition to the important residues located in the active site, residues distal to the active site also contribute to the catalytic activity of the enzyme through stabilizing its structural integrity.

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