{{CHEM_4923_Fall2018}}

This page is reserved for Bo
==Default==
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

==Introduction==
The topic is the study of the enzyme '''glucose oxidase''' (GOX) from '''aspergillus niger'''. It is not an enzyme from human body. Instead, it is found in the cells of fungus. These types of enzymes catalysts the oxidation of beta-D-glucose to δ-gluconolactone and H2O2 (which is not a reaction happening in human body) <ref>PMID:10216293</ref>.

GOX has a “considerable commercial importance” in biosensors according to the essay. This type of enzyme is wildly used in biosensor. Since it could react with glucose with a great selectivity and produce hydrogen peroxide, the amount of hydrogen peroxide is a function of the initial amount of the glucose ideally. For is reason, it is used for quantitively measuring the amount of concentration of glucose, or in a simpler way, measuring the concentration of blood glucose <ref>PMID: 24907743</ref>. Thus, it could be (actually had already been) widely used in quick blood glucose tests, which is essential to those who have diabetes. However, the usage of this enzyme is not exactly limited to the medical area. A good method of reflecting the concentration of glucose could also be used in food industry in measuring and controlling the sugar amount in food samples since most types of natural-sourced carbohydrate in food industry, such as sucrose and lactose, contain glucose <ref>PMID: 19374943</ref>.

Two PDB files mentioned in the essay, 1cf3 and 1gpe, which are two glucose oxidases from different organisms, ''aspergillus niger''' and '''Penicillium Amagasakiense'''. They have exactly the same types of ligands. The most important ligand is FAD cofactor, which assists the oxidation of beta-D-glucose. This essay was published back to 1999, which is fairly old in the scale of science.

== Structure ==
<Structure load='1cf3' size='350' frame='true' align='right' caption='The glucose oxidase from Aspergillus Niger (PDB#:1cf3)' scene='Insert optional scene name here' />

The structure of this PDB file (1cf3) contains only one chain with 4 different types of ligands. This is a 583-residue-long enzyme with a molecular weight of about 65.8kDa. The structure is tested by X-ray diffraction.

Another glucose oxidase also tested with X-ray diffraction method in the same essay from '''Penicillium Amagasakiense''' has two identical chains in the PDB file which is the regular form of this type of enzyme. They have 81% sequence similarity and also very similar structures (which could be seen from the figure below).

[[Image: Different GOX.png]]
Fig. 1 Comparison between the structures of glucose oxidase from aspergillus niger (PDB code:1cf3, the tan part) and penicillium amagasakiense (PDB code: 1gpe, the cyan part). One of the chains of 1gpe was hidden.

Each chain of the enzyme contains a FAD cofactor and the molecules are tightly but non-covalently bonded to the enzyme <ref>PMID: 19374943</ref>. The residues of the active sites, Tyr-73, Phe-418, Trp-430, Arg-516, Asn-518, His-520 and His-563, locate around the cofactor. The cofactors locate at the interface between two chains of the enzyme, covered by an “irregular two-stranded antiparallel-sheet structure formed by residues 75-98”, which prevents the cofactors being released <ref>PMID:10216293</ref>. Generally speaking, the FAD molecules are tightly “covered” or “surrounded” by the enzyme. The binding sites with FAD of both enzymes (GOX’s from Aspergillus niger and Penicillium Amagasakiense) are almost identical with several exceptions of hydrogen-bonds-forming residues His-78 and Thr-110. These two residues are Gln-78 and Ser-100 in the GOX from Penicillium Amagasakiense. Flavin O4’s of the FAD cofactors in both enzymes are connected to the 110th residue (either Thr or Ser) and the Gly-108 residue (Wohlfahrt, 1999).

[[Image:Position of FDA of GOX from PA.png]
Fig. 2 Relative position of two FAD molecules of the penicillium amagasakiense (PDB code: 1gpe) with transparent surface, which will hopefully give a rough image about how the two chains of the enzyme are arranged. Since the 1cf3 file (GOX from aspergillus niger) only have one chain given, the 1gpe (GOX from penicillium amagasakiense) was used instead.

== Function ==
[[Image:MAN and BMA and NAG.png]]
The green part is the dimer of MAN, the blue part is the BMA (one of the reactants) and the yellow part is the a dimer of NAG.
Residues <scene name='80/800656/Asns/1'> Asn89, 161, 355 and 388</scene> (the residues in red) were highlighted by the author because of their interaction with the ligands.
== Energetic ==
FAD acts as an electron carrier during the reaction. The '''GOX-FAD''' form of the enzyme is reduced to the '''GOX-FADH2''' form during the reaction. The FAD oxidizes the β-D-glucose to δ-gluconolactone and being reduced to FADH2; the oxygen molecule is reduced to the hydrogen peroxide with the electrons transferred. This process is supported by a protonated '''His''' residue, which thus functions best at lower pH. Although the mechanism of the reaction had been clearly studied, the actual roles of the residues of the active sites are still unclear <ref>PMID: 10749686</ref>.

</StructureSection>
== References ==
<references/>

Sandbox Reserved 1477

2018-12-14T02:59:10Z

Bo Zhao:

Sandbox Reserved 1477

2018-12-14T02:56:48Z

Bo Zhao:

{{CHEM_4923_Fall2018}}

This page is reserved for Bo
==Default==
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

==Introduction==
The topic is the study of the enzyme '''glucose oxidase''' (GOX) from '''aspergillus niger'''. It is not an enzyme from human body. Instead, it is found in the cells of fungus. These types of enzymes catalysts the oxidation of beta-D-glucose to δ-gluconolactone and H2O2 (which is not a reaction happening in human body) <ref>PMID:10216293</ref>.

GOX has a “considerable commercial importance” in biosensors according to the essay. This type of enzyme is wildly used in biosensor. Since it could react with glucose with a great selectivity and produce hydrogen peroxide, the amount of hydrogen peroxide is a function of the initial amount of the glucose ideally. For is reason, it is used for quantitively measuring the amount of concentration of glucose, or in a simpler way, measuring the concentration of blood glucose <ref>PMID: 24907743</ref>. Thus, it could be (actually had already been) widely used in quick blood glucose tests, which is essential to those who have diabetes. However, the usage of this enzyme is not exactly limited to the medical area. A good method of reflecting the concentration of glucose could also be used in food industry in measuring and controlling the sugar amount in food samples since most types of natural-sourced carbohydrate in food industry, such as sucrose and lactose, contain glucose <ref>PMID: 19374943</ref>.

Two PDB files mentioned in the essay, 1cf3 and 1gpe, which are two glucose oxidases from different organisms, ''aspergillus niger''' and '''Penicillium Amagasakiense'''. They have exactly the same types of ligands. The most important ligand is FAD cofactor, which assists the oxidation of beta-D-glucose. This essay was published back to 1999, which is fairly old in the scale of science.

== Structure ==
<Structure load='1cf3' size='350' frame='true' align='right' caption='The glucose oxidase from Aspergillus Niger (PDB#:1cf3)' scene='Insert optional scene name here' />

The structure of this PDB file (1cf3) contains only one chain with 4 different types of ligands. This is a 583-residue-long enzyme with a molecular weight of about 65.8kDa. The structure is tested by X-ray diffraction.

Another glucose oxidase also tested with X-ray diffraction method in the same essay from '''Penicillium Amagasakiense''' has two identical chains in the PDB file which is the regular form of this type of enzyme. They have 81% sequence similarity and also very similar structures (which could be seen from the figure below).

[[Image: Different GOX.png]]
Fig. 1 Comparison between the structures of glucose oxidase from aspergillus niger (PDB code:1cf3, the tan part) and penicillium amagasakiense (PDB code: 1gpe, the cyan part). One of the chains of 1gpe was hidden.

Each chain of the enzyme contains a FAD cofactor and the molecules are tightly but non-covalently bonded to the enzyme <ref>PMID: 19374943</ref>. The residues of the active sites, Tyr-73, Phe-418, Trp-430, Arg-516, Asn-518, His-520 and His-563, locate around the cofactor. The cofactors locate at the interface between two chains of the enzyme, covered by an “irregular two-stranded antiparallel-sheet structure formed by residues 75-98”, which prevents the cofactors being released <ref>PMID:10216293</ref>. Generally speaking, the FAD molecules are tightly “covered” or “surrounded” by the enzyme. The binding sites with FAD of both enzymes (GOX’s from Aspergillus niger and Penicillium Amagasakiense) are almost identical with several exceptions of hydrogen-bonds-forming residues His-78 and Thr-110. These two residues are Gln-78 and Ser-100 in the GOX from Penicillium Amagasakiense. Flavin O4’s of the FAD cofactors in both enzymes are connected to the 110th residue (either Thr or Ser) and the Gly-108 residue (Wohlfahrt, 1999).

[[Image:Position of FDA of GOX from PA.png]
Fig. 2 Relative position of two FAD molecules of the penicillium amagasakiense (PDB code: 1gpe) with transparent surface, which will hopefully give a rough image about how the two chains of the enzyme are arranged. Since the 1cf3 file (GOX from aspergillus niger) only have one chain given, the 1gpe (GOX from penicillium amagasakiense) was used instead.

== Function ==
[[Image:MAN and BMA and NAG.png]]
The green part is the dimer of MAN, the blue part is the BMA (one of the reactants) and the yellow part is the a dimer of NAG.
Residues <scene name='80/800656/Asns/1'> Asn89, 161, 355 and 388</scene> (the residues in red) were highlighted by the author because of their interaction with the ligands.
== Energetic ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

[[Image:NAG and ASN.png]]
There are totally four NAG ligands (magenta part) around the enzyme which corresponding to the four ASN residues (cyan part) mentioned above, which might be the potential binding sites of the reactants.

</StructureSection>
== References ==
<references/>

Sandbox Reserved 1477

2018-12-14T02:32:54Z

Bo Zhao:

File:Position of FDA of GOX from PA.png

2018-12-05T19:16:45Z

Bo Zhao: Relative position of two FAD molecules of the penicillium amagasakiense (PDB code: 1gpe) with transparent surface. Since the 1cf3 file (GOX from aspergillus niger) only have one chain given, the 1gpe (GOX from penicillium amagasakiense) was used instead.

File:Different GOX.png

2018-12-05T18:46:22Z

Bo Zhao: This is a picture of comparison between the structures of glucose oxidase from aspergillus niger (PDB code:1cf3, the tan part) and penicillium amagasakiense (PDB code: 1gpe, the cyan part). One of the chains of 1gpe was hidden.

== Summary ==
This is a picture of comparison between the structures of glucose oxidase from aspergillus niger (PDB code:1cf3, the tan part) and penicillium amagasakiense (PDB code: 1gpe, the cyan part). One of the chains of 1gpe was hidden.
== Licensing ==
{{PD-self}}

2018-11-12T19:04:43Z

Bo Zhao:

2018-11-05T18:40:09Z

Bo Zhao:

{{CHEM_4923_Fall2018}}

This page is reserved for Bo

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
<Structure load='1cf3' size='350' frame='true' align='right' caption='The glucose oxidase from Aspergillus Niger (PDB#:1cf3)' scene='Insert optional scene name here' />
== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>