Elizeu/sandbox/citocromo c

Introduction:

Alginate binding protein is the protein responsible for mediating the transport of alginate from the pit on the cell surface to the alginate specific ABC (ATP-binding cassette) importer ^[1]. This system of transferring exists in a gram-negative bacterium, Sphingomonas sp. A1^[2]. This protein, which is a periplasmic binding protein, has two homologues AlgQ1 and AlgQ2 coded in PDB as 1Y3N and 1J1N respectively. Alginate is an anionic polysaccharide that is highly found in the cell walls of brown algae. Alginic acid (Alginate) is a linear copolymer with homopolymeric blocks of (1-4)-linked β-D-mannuronate (M) and its C-5 epimer α-L-guluronate (G) residues, linked with covalent bonds. Monomers arrange together in three forms, blocks of consecutive G residues, Blocks of Consecutive M residues and heteropolymeric random sequences of G and M^[3]. Strain A1 directly take in this polymeric molecule into the cytoplasm in a process, an important part of which is alginate-binding proteins. 1Y3N is the structure of this alginate binding protein complexed with an alginate disaccharide. A significant number of ABC transporters analyzed so far are just capable of transporting small molecules with a molecular mass less than 2 kDa ^[4]. In macromolecule assimilation, the macromolecule degrading enzymes play the role of making smaller molecules by breaking macromolecules into pieces, so the living cell can assimilate it. As a result, the alginate ABC importer of strain A1 is unusual in the sense that it can import a macromolecule with an average molecular mass of 26 kDa, without the need to break the macromolecule into smaller parts and the alginate binding protein is the periplasmic binding protein that mediates this transport along with other proteins being active in this specific transporter ^[5]. This structure has , , and Calcium atom. BEM is beta-D-mannuronic acid, and MAV is alpha-D-mannopyranuronic acid. The two-dimensional structure of these two ligands is provided here.

alt=BEM (494) and MAV (495) two-dimensional structures

'This is a summary of how Strain A1 superchannel works to import and degrade alginate. G, L-guluronate; M, D-mannuronate; gene for alginate lyases (A1-I, A1-II and A1-III); catabolite-control protein gene; algS, algM1 and algM2, ABC transporter genes for alginate import; algQ1 and algQ2, genes for alginate-binding proteins; a1-IV, alginate lyase A1-IV gene; a1-II’, alginate lyase A1-II’ gene; a1-IV’, alginate lyase A1-IV’ gene; p3, TonB-dependent transporter; p5, alginate receptor; FlgJ, C-terminal catalytic module for peptidoglycan hydrolysis. Adopted from Hashimoto W, Kawai S, Murata K. Bacterial supersystem for alginate import/metabolism and its environmental and bioenergy applications. Bioeng Bugs. 2010 Mar-Apr;1(2):97-109. doi: 10.4161/bbug.1.2.10322. Epub 2009 Oct, 14. PMID:21326935 doi:http://dx.doi.org/10.4161/bbug.1.2.10322'

Structural Description and insights to function:

The alginate binding protein consists of two main groups and . AlgQ1 and AlgQ2 are two periplasmic proteins with the almost very similar function which is mediating the transport of the substrate and studies show that the primary structure for this two is about 76% similar, although further investigations are yet to be done to clarify the function and structure differences between these two^[6].Here, we just cover the general structure and functions of these two AlgQ1 and AlgQ2 and their binding to carbohydrates (Alginate). The function of a protein is determined by its shape and the shape of a protein is determined by its primary structure (sequence of amino acids). Based on the analysis of the primary structure done by ([1]) and ProtScale (protscale.html), this protein is water soluble secretory, which suggests that it is periplasmic^[7]. The periplasm is a concentrated gel-like matrix in the space between the inner cytoplasmic membrane and the bacterial outer membrane called the periplasmic space in gram-negative bacteria^[8]. The N-terminal sequence of AlgQ1 is REATW (Arginine, Glutamic acid, Alanine, Threonine, Tryptophan). The first 24 amino acid residues play the role of a . A signal peptide is a short peptide including between 16 to 30 amino acids, which is found at the N-terminus of proteins that are destined toward the secretory pathway^[9]. The bulk of this part includes 5 to 16 hydrophobic amino acids. These hydrophobic residues tend to create a single α-helix and are also referred to as “h-region”. there is typically a number of amino acids at the end of the signal peptide that is recognized and cleaved by signal peptidase and therefore named cleavage site^[10]. AlgQ1 in its two forms (Apo and Holo) comprises 490 amino acid residues, indicating that proteins are truncated. The C-terminal amino acid is determined to be Tyrosine. In addition, the amino acid analysis suggests that AlgQ1 is truncated between Tyr490 and Gly491^[11].We can see the apo-AlgQ1 as a cartoon presentation, made up of N domain and c domain, consisting of residues 1-133, 310-400 and 134-309, 401-490 respectively. The two domains that we introduced are connected to each other through 3 loop segments consisting of residues 133-136, 292-347, and 399-401. The disaccharide is bound to the deep cleft between N and C domains. As mentioned in CATH classification, these two domain both are in a class of alpha/beta proteins, showing 3-Layer(aba) Sandwich architecture, having the topology of D-Maltodextrin-Binding Proteins; domain 2 and the homology of both of these domains as can be predicted is Periplasmic binding protein-like II. If we want to assess how SCOP classify this protein, we can see that SCOP sees this protein as a one domain totally, but the same as in CATH, from the alpha and beta proteins. In addition, this protein belongs to Periplasmic binding protein-like superfamily and comes from Phosphate binding protein-like family^[12][13]. When N-domains of apo and holo forms of the protein were superimposed, then a rotation angle of 0.6 degrees was needed for the C domain to be superimposed. Structures of a holo-AlgQ with tetrasaccharide and disaccharide (AlgQ1) are almost the same^[14]. Here we can see the binding sites holo-algQ1-DI. This bound consists of ΔM1-M2 with α-anomeric M2 at S1 and S2. ΔM, M, and G denote unsaturated D-mannuronate, saturated D-mannuronate, and saturated L-guluronate, respectively. The bound oligosaccharides interact with surrounding amino acids. As Keiko momma, et al. summarized hydrogen bond interactions between the bound alginate oligosaccharides and alginate binding proteins(data not shown) The number of direct hydrogen bonds between AlgQ1 and the disaccharide in holo-AlgQ1 DI is 11 and the number of associated water molecules is 10. Five water molecules are located at S3 and S4 subsites in holo-AlgQ1-DI. The number of C-C contacts that AlgQ1 and disaccharide holo-AlgQ1-DI have is 30, which indicates that the nonreducing end of sugar is in a significant involvement with AlgQ1^[15]. Ramachandran plot analysis shows that most non-glycine residues are located in the most favorable regions. There is only one exception to this, which is Lys251, (apo-AlgQ1, φ=65° and ψ=-141°; holo-AlgQ1-TE, φ=62° and ψ=-133°; and holo-AlgQ1-DI (1Y3N), φ=65° and ψ=-139°), and it is present in an allowed region. Lys251 is located next to the terminus of a helix (H12/C)^[16].

The crystal structure of AlgQ2 consist of two domains separated by a cleft and binds and releases alginate tetrasaccharide by creating conformational change in these two domains^[17]. To mention some of the different forms of this protein we can take a look at 5H6U, 5H71, 1KWH, 1J1N in PDB.The As an alginate binding protein, the dissociation constants are 6 μg/mL for AlgQ1 and 4 μg/mL for AlgQ2.Results from UV absorption spectroscopy indicate that both of these proteins are alginate specific^[18].

Links to available structures

Alginate binding periplasmic structures with binding to different alginate polymers

[2] :1Y3N

[3] :1Y3P

[4] :1Y3Q

[5] :1KWH

[6] :1J1N

[7] :3A09

[8] :3VLU

[9] :3VLV

[10]: 3VLW

[11] :5H6U

[12]

Link to evolutionary related Structures

By running the protein through Consurf ([13]), the Phylogenetic tree of 1Y3N can be obtained. Below a link to this tree is provided. [14]

The is shown here.

References:

1. ↑ Momma K, Mishima Y, Hashimoto W, Mikami B, Murata K. Direct evidence for Sphingomonas sp. A1 periplasmic proteins as macromolecule-binding proteins associated with the ABC transporter: molecular insights into alginate transport in the periplasm. Biochemistry. 2005 Apr 5;44(13):5053-64. PMID:15794643 doi:10.1021/bi047781r
2. ↑ White DC, Sutton SD, Ringelberg DB. The genus Sphingomonas: physiology and ecology. Curr Opin Biotechnol. 1996 Jun;7(3):301-6. PMID:8785434
3. ↑ Lee KY, Mooney DJ. Alginate: properties and biomedical applications. Prog Polym Sci. 2012 Jan;37(1):106-126. doi: 10.1016/j.progpolymsci.2011.06.003. PMID:22125349 doi:http://dx.doi.org/10.1016/j.progpolymsci.2011.06.003
4. ↑ Davidson AL, Chen J. ATP-binding cassette transporters in bacteria. Annu Rev Biochem. 2004;73:241-68. doi: 10.1146/annurev.biochem.73.011303.073626. PMID:15189142 doi:http://dx.doi.org/10.1146/annurev.biochem.73.011303.073626
5. ↑ Boos W, Shuman H. Maltose/maltodextrin system of Escherichia coli: transport, metabolism, and regulation. Microbiol Mol Biol Rev. 1998 Mar;62(1):204-29. PMID:9529892
6. ↑ Momma K, Mishima Y, Hashimoto W, Mikami B, Murata K. Direct evidence for Sphingomonas sp. A1 periplasmic proteins as macromolecule-binding proteins associated with the ABC transporter: molecular insights into alginate transport in the periplasm. Biochemistry. 2005 Apr 5;44(13):5053-64. PMID:15794643 doi:10.1021/bi047781r
7. ↑ Momma K, Mishima Y, Hashimoto W, Mikami B, Murata K. Direct evidence for Sphingomonas sp. A1 periplasmic proteins as macromolecule-binding proteins associated with the ABC transporter: molecular insights into alginate transport in the periplasm. Biochemistry. 2005 Apr 5;44(13):5053-64. PMID:15794643 doi:10.1021/bi047781r
8. ↑ Miller SI, Salama NR. The gram-negative bacterial periplasm: Size matters. PLoS Biol. 2018 Jan 17;16(1):e2004935. doi: 10.1371/journal.pbio.2004935., eCollection 2018 Jan. PMID:29342145 doi:http://dx.doi.org/10.1371/journal.pbio.2004935
9. ↑ Kapp, Katja; Schrempf, Sabrina; Lemberg, Marius K.; Dobberstein, Bernhard (2013-01-01). Post-Targeting Functions of Signal Peptides. Landes Bioscience.
10. ↑ Momma K, Mishima Y, Hashimoto W, Mikami B, Murata K. Direct evidence for Sphingomonas sp. A1 periplasmic proteins as macromolecule-binding proteins associated with the ABC transporter: molecular insights into alginate transport in the periplasm. Biochemistry. 2005 Apr 5;44(13):5053-64. PMID:15794643 doi:10.1021/bi047781r
11. ↑ Momma K, Mishima Y, Hashimoto W, Mikami B, Murata K. Direct evidence for Sphingomonas sp. A1 periplasmic proteins as macromolecule-binding proteins associated with the ABC transporter: molecular insights into alginate transport in the periplasm. Biochemistry. 2005 Apr 5;44(13):5053-64. PMID:15794643 doi:10.1021/bi047781r
12. ↑ Momma K, Mishima Y, Hashimoto W, Mikami B, Murata K. Direct evidence for Sphingomonas sp. A1 periplasmic proteins as macromolecule-binding proteins associated with the ABC transporter: molecular insights into alginate transport in the periplasm. Biochemistry. 2005 Apr 5;44(13):5053-64. PMID:15794643 doi:10.1021/bi047781r
13. ↑ http://www.cathdb.info/
14. ↑ Momma K, Mishima Y, Hashimoto W, Mikami B, Murata K. Direct evidence for Sphingomonas sp. A1 periplasmic proteins as macromolecule-binding proteins associated with the ABC transporter: molecular insights into alginate transport in the periplasm. Biochemistry. 2005 Apr 5;44(13):5053-64. PMID:15794643 doi:10.1021/bi047781r
15. ↑ Momma K, Mishima Y, Hashimoto W, Mikami B, Murata K. Direct evidence for Sphingomonas sp. A1 periplasmic proteins as macromolecule-binding proteins associated with the ABC transporter: molecular insights into alginate transport in the periplasm. Biochemistry. 2005 Apr 5;44(13):5053-64. PMID:15794643 doi:10.1021/bi047781r
16. ↑ Momma K, Mishima Y, Hashimoto W, Mikami B, Murata K. Direct evidence for Sphingomonas sp. A1 periplasmic proteins as macromolecule-binding proteins associated with the ABC transporter: molecular insights into alginate transport in the periplasm. Biochemistry. 2005 Apr 5;44(13):5053-64. PMID:15794643 doi:10.1021/bi047781r
17. ↑ Hashimoto W, Kawai S, Murata K. Bacterial supersystem for alginate import/metabolism and its environmental and bioenergy applications. Bioeng Bugs. 2010 Mar-Apr;1(2):97-109. doi: 10.4161/bbug.1.2.10322. Epub 2009 Oct, 14. PMID:21326935 doi:http://dx.doi.org/10.4161/bbug.1.2.10322
18. ↑ Momma K, Mishima Y, Hashimoto W, Mikami B, Murata K. Direct evidence for Sphingomonas sp. A1 periplasmic proteins as macromolecule-binding proteins associated with the ABC transporter: molecular insights into alginate transport in the periplasm. Biochemistry. 2005 Apr 5;44(13):5053-64. PMID:15794643 doi:10.1021/bi047781r