User:Gabriel Pons/Sandbox 2: Difference between revisions

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<StructureSection load='1cpu' size='400' side='right' scene='42/428167/Vision_general/1' caption='Amilasa con los aminoácidos del centro activo (rojo) (PDB code 1cpu)'>
<scene name='42/428167/Alanina-1-1/1'>Aminoácido tipo de las proteínas </scene>
=Centro activo=
La amilasa pancreática es una endoglicosidasa que hidroliza enlaces alfa 1-4 de poliglícidos de glucosa
 
para entender porqué solamente ataca los enlaces interiores del poliglícido es necesario ver cómo se coloca el poliglícido al unirse al centro activo . 1cpu muestra la estructura de la amilasa pancreática . El <scene name='42/428167/Centro_activo/2'>centro activo </scene>se muestra ocupado por 5 unidades glicídicas que son abrazadas por la hendidura del centro activo . En rojo se muestran los dos aminoácidos principales que participan en la catálisis, aspártico 197 y glutámico 233
 
The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel  β-strands. Long loops are observed between the β-strands.  Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca<sup>2+</sup>-Na<sup>+</sup>-Ca<sup>2+</sup>. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands is assembled into a globular unit forming a Greek key motif.  It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca<sup>2+</sup> binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)<sub>8</sub>-barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are
<scene name='Sandbox_182/Active_site/1'>Asp234, Glu264, and Asp331</scene>. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/2'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca<sup>2+</sup> ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from α6 of domain A, and one between β1 and β2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.
 
=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.
 
==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.
 
==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures<ref name="inhibit">PPMID: 17713601</ref>. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref name="inhibit"/>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.
 
=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping.  After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>.  Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure<ref>PMID: 16286272 </ref>. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains<ref name="book"/>.
β/α amylase (BAAM) is a precursor protein which is cleaved to form the β-amylase and α-amylase after secretion.
</StructureSection>
 
==3D structures of amylase (Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}) ==
{{#tree:id=OrganizedByTopic|openlevels=0|
* α-amylase
** [[3ij7]], [[1xv8]], [[1c8q]], [[1bsi]], [[1smd]], [[1hny]] – hAAM – human
** [[1xgz]], [[1q4n]], [[1kb3]], [[1kbb]], [[1kbk]], [[1kgu]], [[1kgw]], [[1kgx]], [[1jxj]], [[1jxk]], [[2cpu]] - hAAM (mutant)
** [[3n8t]] – TkAAM – ''Thermococcus kodakarensis''
** [[3k8k]] – BtAAM – ''Bacterioides thetaiotaomicron''
** [[3kwx]], [[2guy]] – AoAAM – ''Aspergilluys oryzae''
** [[2wpg]] – AAM – ''Xanthomonas campestris''
** [[2wc7]], [[2wcs]], [[2wkg]] – AAM catalytic region – ''Cyanobacterium''
** [[3bh4]] – BaAAM – ''Bacillus amyloliquefaciens''
** [[1e3x]], [[1e43]] – BaAAM chimera
** [[1ht6]], [[1amy]] - bAAM – barley
** [[3bsg]] – bAAM (mutant)
** [[3dhu]] – AAM – ''Lactobacillus plantarum''
** [[3dc0]] – AAM – ''Bacillus KR8104''
** [[3bcf]], [[1wza]] – HoAAM – ''Halothermothrix orenii''
** [[2die]], [[1wp6]] – AAM alkaline – ''Bacillus sp.''
** [[1ud2]], [[1ud4]], [[1ud5]], [[1ud6]], [[1ud8]] - AAM – ''Bacillus sp. KSM-K38''
** [[1ud3]] – AAM (mutant) – ''Bacillus sp. KSM-K38''
** [[2gjr]] – BhAAM – ''Bacillus halmapalus''
** [[2b5d]] – AAM – ''Thermotoga maritima''
** [[2c3g]], [[2c3v]] – BhaloAAM – ''Bacillus halodurans''
** [[1ji1]], [[1ji2]], [[1bvz]] - TvAAM – ''Thermoactinomyces vulgaris''
** [[1wzk]], [[1wzl]], [[1wzm]], [[1izj]], [[1izk]], [[1jf5]], [[1jf6]] – TvAAM (mutant)
** [[1mwo]], [[1mxd]] – PwAAM – ''Pyrococcus woesei''
** [[1ob0]], [[1bli]] - BlAAM (mutant) – ''Bacillus licheniformis''<br />
** [[1vjs]] – BlAAM precursor<br />
** [[1bpl]] – BlAAM<br />
** [[1b0i]], [[1aqm]], [[1aqh]] – PhAAM - ''Pseudoalteromonas haloplanktis''
** [[1jd7]], [[1jd9]] - PhAAM (mutant)
** [[1g5a]] – NpAAM – ''Neisseria polysaccharea''
** [[1hvx]] - BaAAM – ''Bacillus stearothermophilus''
** [[1qho]] – GsAAM – ''Geobacillus stearothermophilus''
** [[1jae]] – TmAAM – ''Tenebrio molitor''
** [[1pif]] – pAAM – pig
** [[6taa]], [[2aaa]] - AoAAM<br />
** [[4aee]] – AAM catalytic domain – ''Staphylothermus marinus''<br />
** [[3ren]] – AAM – ''Clostridium perfringens''<br />
** [[3vm5]] – AAM – ''Oryzias latipes''<br />
** [[3vm7]] – AAM – ''Malbranchea cinnamomea''<br />
** [[4gkl]] – AAM – ''Thermotoga neapolitana''<br />
** [[4ays]] – AAM – ''Deinococcus radiodurans''<br />
** ''AAM binary complexes''
*** [[1xd0]], [[1xd1]], [[1cpu]], [[1jfh]] - hAAM + saccharide<br />
*** [[1b2y]], [[1xcw]], [[1xcx]] - hAAM + acarbose<br />
*** [[3blk]], [[3blp]], [[1z32]], [[1nm9]], [[1mfu]], [[1mfv]], [[3cpu]] - hAAM (mutant) + saccharide<br />
*** [[3dhp]], [[1xh0]], [[1xh2]] - hAAM (mutant) + acarbose<br />
*** [[3ij8]], [[3ij9]] – hAAM catalytic intermediate
*** [[2qmk]], [[3bai]] – hAAM + NO2
*** [[3baw]] – hAAM + N3
*** [[3bax]] - hAAM (mutant) + N3
*** [[3bak]] – hAAM (mutant) + NO3
*** [[1xh1]] - hAAM (mutant) + Cl
*** [[2qv4]], [[3baj]], [[3bay]] - hAAM + acarbose + NO2
*** [[3old]], [[3ole]], [[3olg]], [[3oli]] – hAAM + statin
*** [[1u2y]], [[1u30]], [[1u33]] – hAAM + inhibitor<br />
*** [[4gqq]] – hAAM + ethyl caffeate<br />
*** [[4gqr]] – hAAM + myricetin<br />
*** [[3n92]], [[3n98]] – TkAAM + saccharide<br />
*** [[3l2l]], [[3l2m]], [[1vah]], [[1wo2]], [[1ua3]], [[1pig]], [[1ppi]] - pAAM + saccharide<br />
*** [[1hx0]] – pAAM + acarbose<br />
*** [[1kxq]], [[1kxt]], [[1kxv]] – pAAM + antibody VHH fragment
*** [[1bvn]], [[1dhk]] – pAAM + protein inhibitor
*** [[1ose]] – pAAM + acarbose<br />
*** [[3k8l]] - BtAAM (mutant) + saccharide<br />
*** [[3k8m]] - BtAAM + acarbose<br />
*** [[2d2o]], [[1jl8]], [[1jib]] - TvAAM + saccharide<br />
*** [[3a6o]] – TvAAM + acarbose<br />
*** [[2d0f]], [[2d0g]], [[2d0h]], [[1vb9]], [[1vfm]], [[1vfo]], [[1vfu]], [[1uh2]], [[1uh4]] - TvAAM (mutant) + saccharide<br />
*** [[1uh3]] - TvAAM (mutant) + acarbose<br />
*** [[1ava]] – bAAM + protein inhibitor
*** [[1bg9]], [[1rpk]] - bAAM + acarbose<br />
*** [[1p6w]] – bAAM + substrate analog
*** [[1rp8]], [[1b1y]], [[1rp9]] - bAAM (mutant) + saccharide<br />
*** [[3bsh]], [[2qpu]], [[2qps]] - bAAM (mutant) + acarbose<br />
*** [[3bcd]] - HoAAM + saccharide<br />
*** [[3bc9]] - HoAAM + acarbose<br />
*** [[2gjp]], [[1w9x]] - BhAAM + saccharide<br />
*** [[2gvy]] - AoAAM + saccharide<br />
*** [[1zs2]], [[1s46]], [[1mvy]], [[1mw0]], [[1mw1]], [[1mw2]], [[1mw3]] - NpAAM (mutant) + saccharide<br />
*** [[1bag]] - BsAAM + saccharide – ''Bacillus subtilis''
*** [[1ua7]] – BsAAM + acarbose<br />
*** [[2d3l]], [[2d3n]] - BacAAM + saccharide – ''Bacillus''
*** [[2c3h]], [[2c3w]], [[2c3x]] - BhaloAAM + saccharide<br />
*** [[1mxg]] - PwAAM + acarbose<br />
*** [[3qgv]] - PwAAM + sucrose<br />
*** [[1g9h]], [[1g94]] - PhAAM + saccharide<br />
*** [[1kxh]] - PhAAM (mutant) + acarbose<br />
*** [[1l0p]] – PhAAM + NO3
*** [[1e40]] – BaAAM chimera + saccharide<br />
*** [[1e3z]] - BaAAM chimera + acarbose<br />
*** [[1fa2]] - AAM + saccharide – Sweet potato
*** [[1qhp]] - GsAAM + saccharide<br />
*** [[4e2o]] - GsAAM + acarbose<br />
*** [[1clv]], [[1viw]], [[1tmq]] – TmAAM + protein inhibitor
*** [[1gah]], [[1gai]] – AaAAM + acarbose – ''Aspergillus awamori''
*** [[3gly]], [[1agm]], [[1glm]] – AaAAM + saccharide<br />
 
* Pullulanase α-amylase
** [[2wan]] – AAM – ''Bacillus acidopullululyticus''
** [[2fgz]] – KaAAM – ''Klebsiella aerogenes''
** [[2e8y]] - BsAAM <br />
** [[1ji2]] - TvAAM <br />
** [[1jl5]], [[1jf6]], [[1wzk]], [[1wzl]], [[1wzm]] - TvAAM (mutant)<br />
 
** ''Pullulanase α-amylase binary complexes''
*** [[2fh6]], [[2fh8]], [[2fhb]], [[2fhc]], [[2fhf]] - KaAAM + saccharide<br />
*** [[3fax]] - AAM + saccharide – ''Streptococcus agalactiae''
*** [[2e8z]], [[2e9b]] - BsAAM + saccharide<br />
*** [[2d2o]] - TvAAM + saccharide<br />
*** [[1g1y]], [[1jib]], [[1jl8]], [[1vfm]], [[1vfo]], [[1vfu]], [[1vb9]] - TvAAM (mutant) + saccharide<br />
*** [[3a6o]] – TvAAM + acarbose <br />
 
* Neopullulanase α-amylase
** [[4aef]] – AAM – ''Pyrococcus furiosus''<br />
** [[1j0h]] – BsAAM<br />
** [[2z1k]] – AAM – ''Thermus thermophilus''<br />
** [[1j0i]] – BsAAM + α-D-glucose<br />
** [[1j0k]] – BsAAM (mutant) + α-D-glucose<br />
** [[1j0j]] – BsAAM (mutant) + maltotetraose<br />
 
* β-amylase
** [[2xfr]] – bBAM
** [[1wdp]] – sBAM – soybean
** [[2dqx]], [[1uko]], [[1ukp]] – sBAM (mutant)
** [[1vem]], [[5bca]], [[1cqy]], [[1b90]] – BcBAM – ''Bacillus cereus''
** [[1ven]] - BcBAM (mutant)<br />
** [[1fa2]] - AAM + saccharide – Sweet potato<br />
 
** ''β-amylase binary complexes''
*** [[2xff]] – bBAM + acarbose<br />
*** [[2xfy]], [[2xg9]], [[2xgb]], [[2xgi]] – bBAM + inhibitor
*** [[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 />
*** [[1b1y]] - AAM (mutant) + saccharide – Hordeum vulgare<br />
 
* γ-amylase
** [[1lf6]] – TtGAM – ''Thermoanaerobacterium thermosaccharolyticum''
** [[1lf9]] - TtGAM + acarbose<br />
 
* β/α-amylase
** [[2laa]], [[2lab]] – PpBAAM – ''Paenibacillus polymyxa'' - NMR<br />
** [[3voc]] – PpBAAM<br />
 
* Maltohexaose-producing amylase
** [[1wp6]] - BacMAM
**[[1wpc]] – BacMAM  + saccharide<br />
 
* Maltogenic amylase
** [[1gvi]], [[1sma]] – MAM – ''Thermus sp.''
 
* Taka amylase
** [[2taa]], [[3vx0]], [[3vx1]] – AoTAM
** [[7taa]] – AoTAM + acarbose
 
}}
=References=
<references/>
 
[[Category:Topic Page]]
 
[[he:Amylase (Hebrew)]]

Latest revision as of 23:29, 20 December 2017

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