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Difference between revisions of "Carbohydrate Binding Module Family 74"
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| − | * [[Author]]: | + | * [[Author]]: [[User:Amanda Photenhauer|Amanda Photenhauer]] |
| − | * [[Responsible Curator]]: | + | * [[Responsible Curator]]: [[User:Nicole Koropatkin|Nicole Koropatkin]] |
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| − | + | CBM74 is a starch-binding CBM that was originally characterized as a discreet domain of a raw starch degrading amylase from the bacterium, ''Microbacterium aurum''. ''Microbacterium aurum'' was isolated from the waste sludge of a potato starch processing facility so it may be no surprise that ''Ma''CBM74 binds raw potato, corn, and wheat starches. CBM74 doesn't fit the paradigm of CBMs in that it consists of 300-350 amino acids as opposed to the canonical 100-150 amino acids. The molecular basis for binding remains unknown. | |
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --> | <!-- The data in the table below should be updated by the Author/Curator according to current information on the family --> | ||
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== Ligand specificities == | == Ligand specificities == | ||
| − | The dialysis refolded MaAmyA CBM74 domain was shown to bind to soluble potato starch, boiled granular potato, wheat, and waxy corn starch (type 3 resistant starches) as well as amylose (unspecified source), and amylopectin (unspecified source) by polysaccharide‐binding macroarray. This domain also binds to raw granular starches (type 2 resistant starch) from potato, wheat, and waxy corn as shown by adsorption depletion. CBM74 showed a higher affinity for potato derived starch over that from wheat and maize suggesting that the CBM74 domain has a higher affinity for starches with A-type crystallinity over B-type <cite> Valk2016 </cite> | + | The dialysis refolded MaAmyA CBM74 domain was shown to bind to soluble potato starch, boiled granular potato, wheat, and waxy corn starch (type 3 resistant starches) as well as amylose (unspecified source), and amylopectin (unspecified source) by polysaccharide‐binding macroarray. This domain also binds to raw granular starches (type 2 resistant starch) from potato, wheat, and waxy corn as shown by adsorption depletion. CBM74 showed a higher affinity for potato derived starch over that from wheat and maize suggesting that the CBM74 domain has a higher affinity for starches with A-type crystallinity over B-type<cite> Valk2016 </cite>. |
== Structural Features == | == Structural Features == | ||
| − | CBM74 is predicted to be a discrete domain of approximately 300 amino acids. No CBM74 three dimensional structure has yet been determined | + | CBM74 is predicted to be a discrete domain of approximately 300 amino acids. No CBM74 three dimensional structure has yet been determined. The most similar predicted structure is that of CBM9 from of a xylanase from <i>Thermotoga maritima</i> MSB8<cite> Valk2016 </cite>. Trp71 of CBM9 is conserved among all identified CBM74 domains and may be involved in starch binding<cite>Janecek2019</cite>. |
== Functionalities == | == Functionalities == | ||
| − | + | ||
* '''Functional role of CBM:''' Aside from starch binding, additional roles of CBM74 in raw starch degradation remain unclear. The deletion of the CBM74 domain of MaAmyA resulted in smaller, but not fewer, pores on starch granules as shown by Scanning Electron Microscopy <cite> Valk2016 </cite>. This suggests that CBM74 may contribute to local polysaccharide chain disruption or may keep the enzyme in close proximity to the areas that have already been hydrolyzed. | * '''Functional role of CBM:''' Aside from starch binding, additional roles of CBM74 in raw starch degradation remain unclear. The deletion of the CBM74 domain of MaAmyA resulted in smaller, but not fewer, pores on starch granules as shown by Scanning Electron Microscopy <cite> Valk2016 </cite>. This suggests that CBM74 may contribute to local polysaccharide chain disruption or may keep the enzyme in close proximity to the areas that have already been hydrolyzed. | ||
* '''Most Common Associated Modules:''' | * '''Most Common Associated Modules:''' | ||
:1. Glycoside Hydrolase: CBM74 is a starch-binding CBM and as such is associated only with GH13 domains. The GH13 subfamilies are listed in the table above. So far, two CBM74-containing proteins have been characterized. | :1. Glycoside Hydrolase: CBM74 is a starch-binding CBM and as such is associated only with GH13 domains. The GH13 subfamilies are listed in the table above. So far, two CBM74-containing proteins have been characterized. | ||
| − | ::In some cases CBM74 is not appended to any GH13 domain. For example, | + | ::In some cases CBM74 is not appended to any GH13 domain. For example, Sas6 from the bacterium ''Ruminococcus bromii'' has a CBM26, a CBM74, and a dockerin domain for cohesin-dockerin protein assembly, possibly with a GH13-containing protein. |
:2. CBM25 or CBM26: In every CBM74 domain listed in the CAZy database encodes an adjacent CBM25 or CBM26 domain. | :2. CBM25 or CBM26: In every CBM74 domain listed in the CAZy database encodes an adjacent CBM25 or CBM26 domain. | ||
| − | :3. FNIII or Bacterial Ig-like2 | + | :3. FNIII (FN3) or Bacterial Ig-like2 (BIG2) |
== Family Firsts == | == Family Firsts == | ||
;First Identified | ;First Identified | ||
Latest revision as of 16:39, 22 May 2023
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
CBM74 is a starch-binding CBM that was originally characterized as a discreet domain of a raw starch degrading amylase from the bacterium, Microbacterium aurum. Microbacterium aurum was isolated from the waste sludge of a potato starch processing facility so it may be no surprise that MaCBM74 binds raw potato, corn, and wheat starches. CBM74 doesn't fit the paradigm of CBMs in that it consists of 300-350 amino acids as opposed to the canonical 100-150 amino acids. The molecular basis for binding remains unknown.
| Carbohydrate Binding Module Family 74 | |
| Carbohydrate Specificity | Starch |
| Associated GH Families | GH13_28 GH13_19 GH13_32 none |
| CAZy DB link | |
| https://www.cazy.org/CBM74.html | |
Ligand specificities
The dialysis refolded MaAmyA CBM74 domain was shown to bind to soluble potato starch, boiled granular potato, wheat, and waxy corn starch (type 3 resistant starches) as well as amylose (unspecified source), and amylopectin (unspecified source) by polysaccharide‐binding macroarray. This domain also binds to raw granular starches (type 2 resistant starch) from potato, wheat, and waxy corn as shown by adsorption depletion. CBM74 showed a higher affinity for potato derived starch over that from wheat and maize suggesting that the CBM74 domain has a higher affinity for starches with A-type crystallinity over B-type[1].
Structural Features
CBM74 is predicted to be a discrete domain of approximately 300 amino acids. No CBM74 three dimensional structure has yet been determined. The most similar predicted structure is that of CBM9 from of a xylanase from Thermotoga maritima MSB8[1]. Trp71 of CBM9 is conserved among all identified CBM74 domains and may be involved in starch binding[2].
Functionalities
- Functional role of CBM: Aside from starch binding, additional roles of CBM74 in raw starch degradation remain unclear. The deletion of the CBM74 domain of MaAmyA resulted in smaller, but not fewer, pores on starch granules as shown by Scanning Electron Microscopy [1]. This suggests that CBM74 may contribute to local polysaccharide chain disruption or may keep the enzyme in close proximity to the areas that have already been hydrolyzed.
- Most Common Associated Modules:
- 1. Glycoside Hydrolase: CBM74 is a starch-binding CBM and as such is associated only with GH13 domains. The GH13 subfamilies are listed in the table above. So far, two CBM74-containing proteins have been characterized.
- In some cases CBM74 is not appended to any GH13 domain. For example, Sas6 from the bacterium Ruminococcus bromii has a CBM26, a CBM74, and a dockerin domain for cohesin-dockerin protein assembly, possibly with a GH13-containing protein.
- 2. CBM25 or CBM26: In every CBM74 domain listed in the CAZy database encodes an adjacent CBM25 or CBM26 domain.
- 3. FNIII (FN3) or Bacterial Ig-like2 (BIG2)
Family Firsts
- First Identified
- CBM74 was first identified as the C-terminal domain of a multi-modular α-amylase, MaAmyA, originating from Microbacterium aurum[1].
- First Structural Characterization
- No structure has yet been determined for any CBM74 family member.
References
- Valk V, Lammerts van Bueren A, van der Kaaij RM, and Dijkhuizen L. (2016). Carbohydrate-binding module 74 is a novel starch-binding domain associated with large and multidomain α-amylase enzymes. FEBS J. 2016;283(12):2354-68. DOI:10.1111/febs.13745 |
- Janeček Š, Mareček F, MacGregor EA, and Svensson B. (2019). Starch-binding domains as CBM families-history, occurrence, structure, function and evolution. Biotechnol Adv. 2019;37(8):107451. DOI:10.1016/j.biotechadv.2019.107451 |
- Candussio A, Schmid G, and Böck A. (1990). Biochemical and genetic analysis of a maltopentaose-producing amylase from an alkaliphilic gram-positive bacterium. Eur J Biochem. 1990;191(1):177-85. DOI:10.1111/j.1432-1033.1990.tb19108.x |
- Candussio A, Schmid G, and Böck A. (1991). Comparative study of the structure/function relationship of wild-type and structurally modified maltopentaose-producing amylase. Eur J Biochem. 1991;199(3):637-41. DOI:10.1111/j.1432-1033.1991.tb16164.x |