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| <StructureSection load='' size='350' side='right' scene='Sandbox_182/Alpha-amylase/1' caption='Amylase complex with Ca+2 (green) and Na+ (purple) ions (PDB code [[1hvx]])'> | | <StructureSection load='' size='350' side='right' scene='Sandbox_182/Alpha-amylase/1' caption='Amylase complex with Ca+2 (green) and Na+ (purple) ions (PDB code [[1hvx]])'> |
| =Introduction= | | =Introduction= |
| Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>.'''α-Amylase''' (AAM) is an enzyme that acts as a catalyst for the hydrolysis of α-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and saliva<ref name="Path"/>. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries. '''β/α amylase''' (BAAM) is a precursor protein which is cleaved to form the β-amylase and α-amylase after secretion.<br /> | | Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, '''amylase''' was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>.'''α-Amylase''' (AAM) is an enzyme that acts as a catalyst for the hydrolysis of α-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and saliva<ref name="Path"/>. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries. '''β/α amylase''' (BAAM) is a precursor protein which is cleaved to form the β-amylase and α-amylase after secretion. '''β amylase''' (BAM) acts at the non-reducing chain ends and liberate only β-maltose<ref>PMID:6168260</ref>. '''γ amylase''' (GAM) acts at the non-reducing chain ends of amylose and amylopectin and liberates glucose. '''Pullulanase''' hydrolyses the α-1,6 glucoside linkage in starch, amylopectin, pullulan and related oligosaccharides<ref>PMID:22991654</ref>.<br /> |
| | *'''Neopullulanase''' is involved in starch degrading<ref>PMID:8955399</ref>.<br /> |
| For α-amylase see [[Raghad zoubi]]<br /> | | For α-amylase see [[Raghad zoubi]]<br /> |
| See also [[Amylase (Hebrew)]]. | | See also [[Amylase (Hebrew)]]. |
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| β/α amylase (BAAM) is a precursor protein which is cleaved to form the β-amylase and α-amylase after secretion. | | β/α amylase (BAAM) is a precursor protein which is cleaved to form the β-amylase and α-amylase after secretion. |
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| ==3D structures of amylase== | | = Structure of the AmyC GH13 alpha-amylase from Alicyclobacillus sp, reveals accommodation of starch branching points in the alpha-amylase family<ref>doi 10.1107/S2059798318014900</ref> = |
| [[Amylase 3D structures]]
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| </StructureSection>
| | The enzymatic degradation of starch has a myriad industrial applications. However, the branched nature of the polysaccharides that compose it poses problems, as branches have to be accommodated within an active centre best suited to linear polysaccharides. Alpha-amylases are glycoside hydrolases that break the α-1,4 bonds in starch and related glycans. The present work provides a rare insight into branch-point acceptance in these industrial catalysts. |
| ==3D structures of amylase==
| |
| Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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| {{#tree:id=OrganizedByTopic|openlevels=0|
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| * α-amylase
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|
| ** [[3n8t]] – TkAAM – ''Thermococcus kodakarensis''
| | The complex of α-amylase from ''Alicyclobacillus sp.'' 18711 (AliC) with acarbose was solved by molecular replacement, with two molecules of AliC in the asymmetric unit, at a resolution of 2.1 Å ([[6gxv]]). The fold, as expected, is a canonical <scene name='79/799580/Cv1/5'>three-domain arrangement</scene> with the A, B and C domains defined approximately as <span style="color:deepskyblue;background-color:black;font-weight:bold;">A, residues 4–104 and 210–397 (in deepskyblue)</span>, <span style="color:yellow;background-color:black;font-weight:bold;">B, residues 105–209 (in yellow)</span>, and <span style="color:white;background-color:black;font-weight:bold;">C, residues 398–484 (in white)</span>. A classical Ca<sup>2+</sup>–Na<sup>+</sup>–Ca<sup>2+</sup> <scene name='79/799580/Cv1/4'>triad</scene> <ref name="Machius">PMID:9551551</ref>,<ref name="Brzozowski">PMID:10924103</ref> is found at the A/B-domain interface. The structure of AliC was determined in the presence of the <scene name='79/799580/Cv1/6'>inhibitor acarbose</scene> (<span style="color:lime;background-color:black;font-weight:bold;">colored in green</span>). As with many (retaining) α-amylase complexes, the acarbose is observed as a transglycosylated species, here a hexasaccharide which contains two of the acarviosin disaccharide motifs. The <scene name='79/799580/Cv/11'>complex defines six subsites</scene>, -4 to +2, with the expected catalytic GH13 signature triad of Asp234 (nucleophile), Glu265 (acid/base) and <scene name='79/799580/Cv/13'>Asp332 (interacting with O2/O3 of the -1 subsite sugar)</scene> all disposed for catalysis, here around the <sup>2</sup>H<sub>3</sub> half-chair of the unsaturated cyclohexitol moiety. AliC must also be able to accommodate branching in the +2 subsite, which is consistent with the <scene name='79/799580/Cv/14'>glucose moiety seen adjacent to O6 of the +2 sugar</scene>. |
| ** [[3k8k]] – BtAAM – ''Bacterioides thetaiotaomicron''
| | *<scene name='79/799580/Cv/12'>Asp234 and Glu265 interactions</scene>. |
| ** [[3kwx]], [[2guy]] – AoAAM – ''Aspergilluys oryzae''
| |
| ** [[2wpg]] – AAM – ''Xanthomonas campestris''
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| ** [[2wc7]], [[2wcs]], [[2wkg]] – AAM catalytic region – ''Cyanobacterium''
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| ** [[3bh4]] – BaAAM – ''Bacillus amyloliquefaciens''
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| ** [[1e3x]], [[1e43]] – BaAAM chimera
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| ** [[1ht6]], [[1amy]] - bAAM – barley
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| ** [[3bsg]] – bAAM (mutant)
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| ** [[3dhu]] – AAM – ''Lactobacillus plantarum''
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| ** [[3dc0]], [[1ud2]], [[1ud4]], [[1ud5]], [[1ud6]], [[1ud8]], [[1ud3]] – BacAAM – ''Bacillus KR8104''
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| ** [[3bcf]], [[1wza]] – HoAAM – ''Halothermothrix orenii''
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| ** [[2die]], [[1wp6]] – AAM alkaline – ''Bacillus sp.''
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| ** [[2gjr]] – BhAAM – ''Bacillus halmapalus''
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| ** [[2b5d]] – AAM – ''Thermotoga maritima''
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| ** [[2c3g]], [[2c3v]] – BhaloAAM – ''Bacillus halodurans''
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| ** [[1ji1]], [[1ji2]], [[1bvz]] - TvAAM – ''Thermoactinomyces vulgaris''
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| ** [[1wzk]], [[1wzl]], [[1wzm]], [[1izj]], [[1izk]], [[1jf5]], [[1jf6]] – TvAAM (mutant)
| |
| ** [[1mwo]], [[1mxd]] – PwAAM – ''Pyrococcus woesei''
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| ** [[1ob0]], [[1bli]] - BlAAM (mutant) – ''Bacillus licheniformis''<br />
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| ** [[1vjs]] – BlAAM precursor<br />
| |
| ** [[1bpl]] – BlAAM<br />
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| ** [[1b0i]], [[1aqm]], [[1aqh]] – PhAAM - ''Pseudoalteromonas haloplanktis''
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| ** [[1jd7]], [[1jd9]] - PhAAM (mutant)
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| ** [[1g5a]] – NpAAM – ''Neisseria polysaccharea''
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| ** [[1hvx]] - BaAAM – ''Bacillus stearothermophilus''
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| **[[4uzu]] – BaAAM (mutant) <br />
| |
| ** [[1qho]] – GsAAM – ''Geobacillus stearothermophilus''
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| ** [[1jae]] – TmAAM – ''Tenebrio molitor''
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| ** [[1pif]] – pAAM – pig
| |
| ** [[6taa]], [[2aaa]] - AoAAM<br />
| |
| ** [[4aee]] – AAM catalytic domain – ''Staphylothermus marinus''<br />
| |
| ** [[3ren]] – AAM – ''Clostridium perfringens''<br />
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| ** [[3vm5]] – AAM – ''Oryzias latipes''<br />
| |
| ** [[3vm7]] – AAM – ''Malbranchea cinnamomea''<br />
| |
| ** [[4gkl]] – AAM – ''Thermotoga neapolitana''<br />
| |
| **[[5m99]] – AAM – ''Thermotoga petrophila''<br />
| |
| ** [[4ays]] – AAM – ''Deinococcus radiodurans''<br />
| |
| ** [[3wn6]] – AAM (mutant) – Japonica rice<br />
| |
| **[[5a2a]] - AnAAM - ''Anoxybacillus''<br />
| |
| **[[6az5]] – AAM – ''Eubacterium rectale''<br /> | |
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|
| ** ''AAM saccharide complexes''
| | A ‘branched-ligand’ AliC complex was obtained through co-crystallization, with crystals forming in a new space group. This form diffracted poorly and data could only be obtained to 2.95 Å resolution [[6gya]]). Weak density in the -1 subsite, largely diffuse but greater than would be expected for discrete solvent, remained unmodelled. Density was clearer for a panose trisaccharide with an α-1,4-linked disaccharide in subsites +1 and +2 and, crucially, clear density for an α-1,6 branch accommodated in the +1 subsite, providing a structural context for the limit digest analysis of action on amylopectin starch. The <scene name='79/799580/Cv/15'>binding of the branched oligosaccharide in subsites +1, +2 and +1'</scene> (<span style="color:lime;background-color:black;font-weight:bold;">oligosaccharide colored in green</span>). |
|
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|
| *** [[3n92]], [[3n98]] – TkAAM + saccharide<br />
| | =3D structures of amylase= |
| *** [[3l2l]], [[3l2m]], [[1vah]], [[1wo2]], [[1ua3]], [[1pig]], [[1ppi]] - pAAM + saccharide<br />
| | [[Amylase 3D structures]] |
| *** [[1hx0]] – pAAM + acarbose<br />
| |
| *** [[1ose]] – pAAM + acarbose<br />
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| *** [[3k8l]] - BtAAM (mutant) + saccharide<br />
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| *** [[3k8m]] - BtAAM + acarbose<br />
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| ***[[6bs6]] – BtAAM (mutant) + glucose<br />
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| *** [[2d2o]], [[1jl8]], [[1jib]] - TvAAM + saccharide<br />
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| *** [[3a6o]] – TvAAM + acarbose<br />
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| *** [[2d0f]], [[2d0g]], [[2d0h]], [[1vb9]], [[1vfm]], [[1vfo]], [[1vfu]], [[1uh2]], [[1uh4]] - TvAAM (mutant) + saccharide<br />
| |
| *** [[1uh3]] - TvAAM (mutant) + acarbose<br />
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| *** [[1bg9]], [[1rpk]] - bAAM + acarbose<br />
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| *** [[1p6w]] – bAAM + substrate analog
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| *** [[1rp8]], [[1b1y]], [[1rp9]] - bAAM (mutant) + saccharide<br />
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| *** [[3bsh]], [[2qpu]], [[2qps]] - bAAM (mutant) + acarbose<br />
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| **[[6f9h]], [[6f9j]] - bAAM (mutant) + prodrug<br />
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| **[[6f9l]] - bAAM (mutant) + maltose derivative<br />
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| *** [[3bcd]] - HoAAM + saccharide<br />
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| *** [[3bc9]] - HoAAM + acarbose<br />
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| *** [[2gjp]], [[1w9x]] - BhAAM + saccharide<br />
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| *** [[2gvy]] - AoAAM + saccharide<br />
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| *** [[1zs2]], [[1s46]], [[1mvy]], [[1mw0]], [[1mw1]], [[1mw2]], [[1mw3]] - NpAAM (mutant) + saccharide<br />
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| *** [[1bag]] - BsAAM + saccharide – ''Bacillus subtilis''
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| *** [[1ua7]] – BsAAM + acarbose<br />
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| *** [[2d3l]], [[2d3n]] - BacAAM + saccharide – ''Bacillus''
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| *** [[2c3h]], [[2c3w]], [[2c3x]] - BhaloAAM + saccharide<br />
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| *** [[1mxg]] - PwAAM + acarbose<br />
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| *** [[3qgv]] - PwAAM + sucrose<br />
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| *** [[1g9h]], [[1g94]] - PhAAM + saccharide<br />
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| *** [[1kxh]] - PhAAM (mutant) + acarbose<br />
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| *** [[1e40]] – BaAAM chimera + saccharide<br />
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| *** [[1e3z]] - BaAAM chimera + acarbose<br />
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| *** [[1fa2]] - AAM + saccharide – Sweet potato
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| *** [[1qhp]] - BaAAM + saccharide<br />
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| *** [[4e2o]], [[6ag0]] - BacAAM + acarbose<br />
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| *** [[1gah]], [[1gai]] – AaAAM + acarbose – ''Aspergillus awamori''
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| *** [[3gly]], [[1agm]], [[1glm]] – AaAAM + saccharide<br />
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| *** [[5a2c]], [[5a2b]] - AnAAM + maltose <br />
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| **[[6gya]] - AAM + a-glucose + b-glucose - ''Alicyclosbacillus''<br />
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|
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|
| ** ''AAM other complexes''
| | </StructureSection> |
| | |
| *** [[1kxq]], [[1kxt]], [[1kxv]] – pAAM + antibody VHH fragment
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| *** [[1bvn]], [[1dhk]], [[4x0n]] – pAAM + protein inhibitor
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| *** [[1ava]] – bAAM + protein inhibitor
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| *** [[1l0p]] – PhAAM + NO3
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| *** [[1clv]], [[1viw]], [[1tmq]] – TmAAM + protein inhibitor
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| *Human pancreatic α-amylase
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| **[[3ij7]], [[1bsi]], [[1hny]], [[4x9y]], [[5u3a]] – hAAM – human<br />
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| **[[1xgz]], [[1kb3]], [[1kbb]], [[1kbk]], [[1kgu]], [[1kgw]], [[1kgx]], 2cpu]] - hAAM (mutant) <br />
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| **[[3ij8]], [[3ij9]] – hAAM catalytic intermediate<br />
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| **[[1xd0]], [[1xd1]], [[1cpu]], [[1jfh]] - hAAM + saccharide <br />
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| **[[1b2y]], [[1xcw]], [[1xcx]] - hAAM + acarbose <br />
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| **[[3cpu]], [[5td4]] - hAAM (mutant) + saccharide<br />
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| **[[1xh0]], [[1xh2]] - hAAM (mutant) + acarbose<br />
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| **[[2qv4]], [[3baj]], [[3bay]] - hAAM + acarbose + NO2<br />
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| **[[2qmk]], [[3bai]] – hAAM + NO2<br />
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| **[[3baw]] – hAAM + N3<br />
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| **[[3bax]] - hAAM (mutant) + N3<br />
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| **[[3bak]] – hAAM (mutant) + NO3<br />
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| **[[1xh1]] - hAAM (mutant) + Cl<br />
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| **[[3old]], [[3ole]], [[3olg]], [[3oli]] – hAAM + statin<br />
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| **[[1u2y]], [[1u30]], [[1u33]], [[5emy]], [[5e0f]], [[4w93]] – hAAM + inhibitor <br />
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| **[[5kez]], [[5va9]] – hAAM + peptide inhibitor <br />
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| **[[4gqq]] – hAAM + ethyl caffeate<br />
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| **[[4gqr]] – hAAM + myricetin<br />
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| | |
| *Human salivary α-amylase
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| **[[1smd]], [[1c8q]], [[1xv8]] – hAAM <br />
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| **[[1q4n]], [[1jxj]], [[1jxk]] – hAAM (mutant)<br />
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| **[[3blk]], [[3blp]], [[1z32]], [[1nm9]], [[1mfu]], [[1mfv]] - hAAM (mutant) + saccharide<br />
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| **[[3dhp]] - hAAM (mutant) + acarbose<br />
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| * Pullulanase α-amylase
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| ** [[2wan]] – AAM – ''Bacillus acidopullululyticus''
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| ** [[2fgz]] – KaAAM – ''Klebsiella aerogenes''
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| ** [[2e8y]] - BsAAM <br />
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| ** [[1ji2]] - TvAAM <br />
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| ** [[1jl5]], [[1jf6]], [[1wzk]], [[1wzl]], [[1wzm]] - TvAAM (mutant)<br />
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| ** ''Pullulanase α-amylase binary complexes''
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| *** [[2fh6]], [[2fh8]], [[2fhb]], [[2fhc]], [[2fhf]] - KaAAM + saccharide<br />
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| *** [[3fax]] - AAM + saccharide – ''Streptococcus agalactiae''
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| *** [[2e8z]], [[2e9b]] - BsAAM + saccharide<br />
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| *** [[2d2o]] - TvAAM + saccharide<br />
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| *** [[1g1y]], [[1jib]], [[1jl8]], [[1vfm]], [[1vfo]], [[1vfu]], [[1vb9]] - TvAAM (mutant) + saccharide<br />
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| *** [[3a6o]] – TvAAM + acarbose <br />
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| * Neopullulanase α-amylase
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| ** [[4aef]] – AAM – ''Pyrococcus furiosus''<br />
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| ** [[1j0h]] – BsAAM<br />
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| ** [[2z1k]] – AAM – ''Thermus thermophilus''<br />
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| ** [[1j0i]] – BsAAM + α-D-glucose<br />
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| ** [[1j0k]] – BsAAM (mutant) + α-D-glucose<br />
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| ** [[1j0j]] – BsAAM (mutant) + maltotetraose<br />
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| | |
| * β-amylase
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| ** [[2xfr]] – bBAM
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| ** [[1wdp]] – sBAM – soybean
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| ** [[2dqx]], [[1uko]], [[1ukp]] – sBAM (mutant)
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| ** [[1vem]], [[5bca]], [[1cqy]], [[1b90]] – BcBAM – ''Bacillus cereus''
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| ** [[1ven]] - BcBAM (mutant)<br />
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| ** [[1fa2]] - BAM + saccharide – Sweet potato<br />
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| **[[6ger]] - BAM – wheat<br />
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| | |
| ** ''β-amylase binary complexes''
| |
| *** [[2xff]] – bBAM + acarbose<br />
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| *** [[2xfy]], [[2xg9]], [[2xgb]], [[2xgi]] – bBAM + inhibitor<br />
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| *** [[1b1y]] - bBAM (mutant) + saccharide <br />
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| *** [[1wdq]], [[1wdr]], [[1wds]], [[1v3h]], [[1v3i]], [[1q6d]], [[1q6e]], [[1q6f]], [[1q6g]] - sBAM (mutant) + saccharide<br />
| |
| *** [[1q6c]], [[1bfn]], [[1bya]], [[1byb]], [[1byc]], [[1byd]], [[1btc]] - sBAM + saccharide<br />
| |
| *** [[1j0y]], [[1j0z]], [[1j10]], [[1j11]], [[1j12]], [[1j18]], [[1b9z]] - BcBAM + saccharide<br />
| |
| *** [[1veo]], [[1vep]], [[1itc]] - BcBAM (mutant) + saccharide<br />
| |
| **[[1fa2]], [[5wqu]] - SpBAM + saccharide <br />
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| | |
| * γ-amylase
| |
| ** [[1lf6]] – TtGAM – ''Thermoanaerobacterium thermosaccharolyticum''
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| ** [[1lf9]] - TtGAM + acarbose<br />
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| | |
| * β/α-amylase
| |
| ** [[2laa]], [[2lab]] – PpBAAM – ''Paenibacillus polymyxa'' - NMR<br />
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| ** [[3voc]] – PpBAAM<br />
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| | |
| * Maltohexaose-producing amylase
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| ** [[1wp6]] - BacMAM
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| **[[1wpc]] – BacMAM + saccharide<br />
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| | |
| * Maltogenic amylase
| |
| ** [[1gvi]], [[1sma]] – MAM – ''Thermus sp.''
| |
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| * Taka amylase
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| ** [[2taa]], [[3vx0]], [[3vx1]] – AoTAM
| |
| ** [[7taa]] – AoTAM + acarbose
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|
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|
| }}
| |
| =References= | | =References= |
| <references/> | | <references/> |
