Protein Family Models

Gene:

rcbX

Date:

2024-10-01

N2-fixation sustaining protein CowN is required to maintain N2-dependent growth in the presence of low levels of carbon monoxide. It is thought to act by protecting the N2 fixation ability of the nitrogenase complex [1]. [1]. 21115659. Sustaining N2-dependent growth in the presence of CO.. Kerby RL, Roberts GP;. J Bacteriol. 2011;193:774-777. (from Pfam)

Gene:

cowN

Date:

2024-08-14

This family includes small CPxCG-related zinc finger archaeal proteins, which are typically between 200 and 221 amino acids in length. They are likely to bind DNA and to be potential transcriptional regulators. These zinc fingers are characterised by the specific CPxCG pattern (variants CPxCx and CxxCG) and a second Cys/His pattern potentially more general, being 7-40 residues apart, forming a zinc finger motif. This family contains the specific CxxCG motif and the Cys motif (CPxCx) at the N-terminal. A member of this family, the Nif-regulating protein A Swiss:Q8PW88, contains the patterns CxxCG and HxxxH (the latter unique to this protein, located 24 residues away from the CxxCG pattern) to form the zinc finger motif. It is a DNA-binding protein that enhances the transcription of the nitrogen fixation (nif) operon under nitrogen-limited conditions [1]. [1]. 24930989. The transcriptional activator NrpA is crucial for inducing. nitrogen fixation in Methanosarcina mazei Go1 under. nitrogen-limited conditions.. Weidenbach K, Ehlers C, Schmitz RA;. FEBS J. 2014;281:3507-3522. (from Pfam)

Date:

2024-08-14

This entry represents the probable sensor region of the two component regulator protein NtrY [1]. This region includes four probable transmembrane helices. [1]. 1661370. Characterization of a novel Azorhizobium caulinodans ORS571. two-component regulatory system, NtrY/NtrX, involved in nitrogen. fixation and metabolism.. Pawlowski K, Klosse U, de Bruijn FJ;. Mol Gen Genet. 1991;231:124-138. (from Pfam)

Date:

2024-08-14

This is the C-terminal domain, also known as the beta domain, of Rubsico Assembly Chaperone protein (Raf1). Raf1 is necessary for rubisco to catalyze the rate-limiting step of carbon fixation through carboxylating the five-carbon sugar substrate ribulose-1,5-bisphosphate. The beta domains primary function is dimerization, which is critical for Raf1 to achieve the necessary avidity for complex formation with RbcL (the large complex sub-unbit of Rubsico) assembly intermediates. The beta domain is also involved, to a small extent, in binding to RbcL with use of the lustiness near the beta domain's conserved top surface [1]. [1]. 26237510. Structure and mechanism of the Rubisco-assembly chaperone Raf1.. Hauser T, Bhat JY, Milicic G, Wendler P, Hartl FU, Bracher A,. Hayer-Hartl M;. Nat Struct Mol Biol. 2015;22:720-728. (from Pfam)

Date:

2024-08-14

Dipeptidyl peptidase (DPP) family members 8 and 9 are similar to DPP4, consisting of one N-terminal beta-propeller and a C-terminal alpha/beta hydrolase domain, which form a functional homodimer. This entry represents the N-terminal beta-propeller of DPP8 and 9 which consists of eight blades and enlaces a central round pore. It provides the key arginine residue fundamental for substrate fixation which is located in the R-segment, at the interconnecting loop between blades 1 and 2. Ligand binding to DPP8/9 induces a rearrangement at the active site through a disorder-order transition in a loop segment which includes the key arginine residue and partially folds in an alpha-helix (R-helix) [1]. DPP8 and DPP9 play a role in the immune system and in preadipocyte differentiation. DPP9 is also essential for neonatal survival and plays a role in antigen maturation, cell migration, and cell adhesion. Paper describing PDB structure 6eoo. [1]. 29382749. Structures and mechanism of dipeptidyl peptidases 8 and 9,. important players in cellular homeostasis and cancer.. Ross B, Krapp S, Augustin M, Kierfersauer R, Arciniega M,. Geiss-Friedlander R, Huber R;. Proc Natl Acad Sci U S A. 2018;115:E1437. (from Pfam)

Date:

2024-08-14

This family of phosphoenolpyruvate carboxylases is based on seqeunces not picked up by the model for PEPcase, PF00311. Most of the family members are from Archaea. [1]. 15262949. The phosphoenolpyruvate carboxylase from Methanothermobacter. thermautotrophicus has a novel structure.. Patel HM, Kraszewski JL, Mukhopadhyay B;. J Bacteriol. 2004;186:5129-5137. (from Pfam)

Date:

2024-08-14

DIMCO_N is the N-terminal domain of the gamma (Y) subunit of nitrogenase. An alternative name is NafY_N, for nitrogenase accessory factor Y N-terminal. This region is negatively charged and appears to be necessary for recognising and interacting with the apo state of dinitrogenase. The full-length NafY protein facilitates the transfer of iron-molybdenum cofactor, or FeMo-co, into apodinitrogenase by binding to both. The C-terminal region, family Nitro_FeMo-Co, Pfam:PF02579, is the part that binds to the cofactor, and the N-terminus binds to apodinitrogenase. Nitrogenase is the bacterial enzyme responsible for nitrogen fixation by catalysing the reduction of nitrogen gas (N2) to ammonium in an ATP-dependent manner. It has two components, dinitrogenase and dinitrogenase reductase [1]. [1]. 12754195. The three-dimensional structure of the core domain of Naf Y from. Azotobacter vinelandii determined at 1.8-A resolution.. Dyer DH, Rubio LM, Thoden JB, Holden HM, Ludden PW, Rayment I;. J Biol Chem. 2003;278:32150-32156. (from Pfam)

Date:

2024-08-14

Carboxysome Shell Carbonic Anhydrase is a bacterial carbonic anhydrase localised in the carboxysome, where it converts bicarbonate ions to carbon dioxide for use in carbon fixation. It contains three domains, these being: (1) an N-terminal domain composed primarily of four alpha-helices; (2) a catalytic domain containing a tightly bound zinc ion and (3) a C-terminal domain with weak structural similarity to the catalytic domain [1]. This entry represents the C-terminal domain which consists of a central five-stranded mixed beta-sheet with two helices flanking one side of the sheet and one helix flanking the other side and lacks all the necessary zinc ligand residues [1]. [1]. 16407248. The structure of beta-carbonic anhydrase from the carboxysomal. shell reveals a distinct subclass with one active site for the. price of two.. Sawaya MR, Cannon GC, Heinhorst S, Tanaka S, Williams EB, Yeates. TO, Kerfeld CA;. J Biol Chem. 2006;281:7546-7555. (from Pfam)

Date:

2024-08-14

MtrB-PioB is a family of bacterial putative outer membrane porins. This family, is secreted as part of the pio (phototrophic iron oxidation) operon that has been found to couple the oxidation of ferrous iron [Fe(II)] to reductive CO2 fixation using light energy. PioABC is found in Rhodopseudomonas palustris and MtrB-PioB is likely to be a beta-barrel porin. Similar to other outer membrane porins, PioB and MtrB are predicted to have long loops protruding into the extracellular space and short turns on the periplasmic side [1]. [1]. 17189359. The pio operon is essential for phototrophic Fe(II) oxidation in. Rhodopseudomonas palustris TIE-1.. Jiao Y, Newman DK;. J Bacteriol. 2007;189:1765-1773. (from Pfam)

Date:

2024-08-14

This domain family is found in bacteria and archaea, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF02775. There are two completely conserved residues (A and G) that may be functionally important. PFO is involved in carbon dioxide fixation via a reductive TCA cycle. It forms a heterodimer (alpha/beta). The beta subunit has binding motifs for Fe-S clusters and thiamine pyrophosphate. [1]. 11401501. The genes for anabolic 2-oxoglutarate: ferredoxin oxidoreductase. from Hydrogenobacter thermophilus TK-6.. Yun NR, Arai H, Ishii M, Igarashi Y;. Biochem Biophys Res Commun. 2001;282:589-594. (from Pfam)

Date:

2024-08-14

The members of this family are sequences that are similar to TraC (Swiss:Q84HT8). The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli CFN42 that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42a, which is also known as plasmid pSym as it carries most of the genes required for nodulation and nitrogen fixation by the symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58 [1]. [1]. 12591886. Conjugative transfer of p42a from rhizobium etli CFN42, which is. required for mobilization of the symbiotic plasmid, is regulated. by quorum sensing.. Tun-Garrido C, Bustos P, Gonzalez V, Brom S;. J Bacteriol 2003;185:1681-1692. (from Pfam)

Date:

2024-08-14

This family represents the C-terminus (approximately 80 residues) of a number of bacterial Mo-dependent nitrogenases. These are involved in nitrogen fixation in cyanobacteria [1]. Note that many family members are hypothetical proteins. [1]. 7568132. A second nitrogenase in vegetative cells of a heterocyst-forming. cyanobacterium.. Thiel T, Lyons EM, Erker JC, Ernst A;. Proc Natl Acad Sci U S A 1995;92:9358-9362. (from Pfam)

Date:

2024-08-14

This family consists of several bacterial dinitrogenase reductase ADP-ribosyltransferase (DRAT) proteins. Members of this family seem to be specific to Rhodospirillum, Rhodobacter and Azospirillum species. Dinitrogenase reductase ADP-ribosyl transferase (DRAT) carries out the transfer of the ADP-ribose from NAD to the Arg-101 residue of one subunit of the dinitrogenase reductase homodimer, resulting in inactivation of that enzyme. Dinitrogenase reductase-activating glycohydrolase (DRAG) removes the ADP-ribose group attached to dinitrogenase reductase, thus restoring nitrogenase activity. The DRAT-DRAG system negatively regulates nitrogenase activity in response to exogenous NH4+ or energy limitation in the form of a shift to darkness or to anaerobic conditions [1]. [1]. 11160092. Effect of P(II) and its homolog GlnK on reversible. ADP-ribosylation of dinitrogenase reductase by heterologous. expression of the Rhodospirillum rubrum dinitrogenase reductase. ADP-ribosyl transferase-dinitrogenase reductase-activating. glycohydrolase regula. Zhang Y, Pohlmann EL, Halbleib CM, Ludden PW, Roberts GP;. J Bacteriol 2001;183:1610-1620. (from Pfam)

Date:

2024-08-14

This domain is found mainly in the Cyanobacteria and in Proteobacteria such as the nitrogen-fixing bacterium Azotobacter vinelandii. It is found in Nif11, a protein described in Azotobacter as linked to nitrogen fixation [1]. It also constitutes a leader peptide in Nif11-derived peptides (N11P), which are thought to be post-translationally modified microcins derived from a putative nitrogen-fixing protein [2]. N11P sequences have a classic leader peptide cleavage motif, usually Gly-Gly, which marks the end of family-wide similarity area and the beginning of a low-complexity region rich in Cys, Gly and Ser [2]. [1]. 2644218. Physical and genetic map of the major nif gene cluster from. Azotobacter vinelandii.. Jacobson MR, Brigle KE, Bennett LT, Setterquist RA, Wilson MS,. Cash VL, Beynon J, Newton WE, Dean DR;. J Bacteriol 1989;171:1017-1027.. [2]. 20500830. Expansion of ribosomally produced natural products: a nitrile. hydratase- and Nif11-related precursor family.. Haft DH, Basu MK, Mitchell DA;. BMC Biol. 2010;8:70. (from Pfam)

Date:

2024-08-14

The two Fe ions are each coordinated by two conserved cysteine residues. This domain occurs alone in small proteins such as Bacterioferritin-associated ferredoxin (BFD, Swiss:P13655). The function of BFD is not known, but it may may be a general redox and/or regulatory component involved in the iron storage or mobilisation functions of bacterioferritin in bacteria [1]. This domain is also found in nitrate reductase proteins in association with Nitrite and sulphite reductase 4Fe-4S domain [2] (Pfam:PF01077), Nitrite/Sulfite reductase ferredoxin-like half domain (Pfam:PF03460) and Pyridine nucleotide-disulphide oxidoreductase (Pfam:PF00070). It is also found in NifU nitrogen fixation proteins, in association with NifU-like N terminal domain (Pfam:PF01592) and NifU-like domain [3] (Pfam:PF01106). [1]. 8639572. A [2Fe-2S] protein encoded by an open reading frame upstream of. the Escherichia coli bacterioferritin gene.. Garg RP, Vargo CJ, Cui X, Kurtz DM Jr;. Biochemistry 1996;35:6297-6301.. [2]. 8954950. Spectroscopic and voltammetric characterisation of the. bacterioferritin-associated ferredoxin of Escherichia coli.. Quail MA, Jordan P, Grogan JM, Butt JN, Lutz M, Thomson AJ,. Andrews SC, Guest JR;. Biochem Biophys Res Commun 1996;229:635-642.. [3]. 9889981. Iron storage in bacteria.. Andrews SC;. Adv Microb Physiol 1998;40:281-351. (from Pfam)

Date:

2024-08-14

This family consists of several NifT/FixU bacterial proteins. NifT/FixU is a very small, conserved protein that is found in nif clusters; however, its function is unknown [1]. Although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase although perturbation of nifT expression in K. pneumoniae has only a limited effect on nitrogen fixation [2]. [1]. 25513762. Regulation of Three Nitrogenase Gene Clusters in the. Cyanobacterium Anabaena variabilis ATCC 29413.. Thiel T, Pratte BS;. Life (Basel). 2014;4:944-967.. [2]. 23308282. The NifA-RpoN regulon of Mesorhizobium loti strain R7A and its. symbiotic activation by a novel LacI/GalR-family regulator.. Sullivan JT, Brown SD, Ronson CW;. PLoS One. 2013;8:e53762. (from Pfam)

Date:

2024-08-14

This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [1]. [1]. 11717256. Regulation of gene expression in response to oxygen in Rhizobium. etli: role of FnrN in fixNOQP expression and in symbiotic. nitrogen fixation.. Lopez O, Morera C, Miranda-Rios J, Girard L, Romero D, Soberon. M;. J Bacteriol 2001;183:6999-7006. (from Pfam)

Date:

2024-08-14

This family consists of several Rhizobium FixH like proteins. It has been suggested that suggested that the four proteins FixG, FixH, FixI, and FixS may participate in a membrane-bound complex coupling the FixI cation pump with a redox process catalysed by FixG [1]. [1]. 2536685. Rhizobium meliloti fixGHI sequence predicts involvement of a. specific cation pump in symbiotic nitrogen fixation.. Kahn D, David M, Domergue O, Daveran ML, Ghai J, Hirsch PR,. Batut J;. J Bacteriol 1989;171:929-939. (from Pfam)

Date:

2024-08-14

NifQ is involved in early stages of the biosynthesis of the iron-molybdenum cofactor (FeMo-co) [1], which is an integral part of the active site of dinitrogenase [2]. The conserved C-terminal cysteine residues may be involved in metal binding [1]. [1]. 8316214. Structure of the nifQ gene from Enterobacter agglomerans 333 and. its overexpression in Escherichia coli.. Siddavattam D, Singh M, Klingmuller W;. Mol Gen Genet 1993;239:435-440.. [2]. 7954845. Biosynthesis of the iron-molybdenum cofactor of nitrogenase.. Allen RM, Chatterjee R, Madden MS, Ludden PW, Shah VK;. Crit Rev Biotechnol 1994;14:225-249. (from Pfam)

Date:

2024-08-14