Team:DTU-Denmark/Protein Models

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{{:Team:DTU-Denmark/Templates/StartPage|Protein Models}}
{{:Team:DTU-Denmark/Templates/StartPage|Protein Models}}
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We have determined the structures of some proteins we want our mutants to express. Others could be homology modelled due to existing 3D models that had high similarity to the ones we are working with.
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Formatting to follow
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==Mutant 1==
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[[File:DTU_NirS_NO.png|640px]]
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===AMO===
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NirS dimer with N2 - source [http://www.rcsb.org/pdb/explore/explore.do?structureId=1nno 1NNO]
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[[File:DTU_AMO.png|640px|center]]
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[[File:DTU_NarK.png|640px]]
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Figure 1: Ammonia monooxygenase (AMO). Homology models of all three subunits of AMO.
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NarK monomer with NO2 - source: [http://www.rcsb.org/pdb/explore.do?structureId=4JRE 4JRE]
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At the time of writing none of the three subunits from ''Nitrosomonas Europaea'' are available as 3D structures, so each of the subunits was identified at [http://www.uniprot.org/ UNIPROT], and their sequence was homology modelled using [http://www.cbs.dtu.dk/services/CPHmodels/ CPHmodels-3.2]
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{| class="wikitable"
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|-
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! style="background: silver" |Resource
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! style="background: #66CC00" | AmoA
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! style="background: #2B7C37" | AmoB
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! style="background: #99CC33" | AmoC
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|-
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| Uniprot
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| [http://www.uniprot.org/uniprot/Q04507 Q04507]
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| [http://www.uniprot.org/uniprot/Q04508 Q04508]
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| [http://www.uniprot.org/uniprot/Q82T63 Q82T63]
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|-
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| Template pdb code and chain
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| [http://www.pdb.org/pdb/explore/explore.do?structureId=1yew 1YEW.A]
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| [http://www.pdb.org/pdb/explore/explore.do?structureId=1yew 1YEW.B]
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| [http://www.pdb.org/pdb/explore/explore.do?structureId=3rgb 3RGB.C]
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|-
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|Coverage
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| 90.5
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| 86.2
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| 66.4
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|-
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|E-value
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| 1e-87
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| 3e-67
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| 8e-43
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|}
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The three subunits were combined and aligned to the subunits of the [http://www.pdb.org/pdb/explore/explore.do?structureId=1yew Crystal structure] of particulate methane monooxygenase, hence an overlap of two alpha helices.
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===HAO===
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[[File:DTU_Hao.png|640px|center]]
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Figure 2: Hydroxylamine oxidoreductase - source [http://www.rcsb.org/pdb/explore.do?structureId=1fgj 1FGJ].
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===Cc554===
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[[File:DTU_CycA.png|640px|center]]
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Figure 3: Cytochrome c554 - source [http://www.rcsb.org/pdb/explore.do?structureId=1ft5 1FT5].
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===Ccm552===
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[[File:DTU_Cycx.png|640px|center]]
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Figure 4: Homology model of Ccm552.
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{| class="wikitable"
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|-
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! style="background: silver" |Resource
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! style="background: #66CC00" | Ccm552
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|-
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| Uniprot
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| [http://www.uniprot.org/uniprot/Q50926 Q50926]
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|-
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| Template pdb code and chain
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| [http://www.pdb.org/pdb/explore/explore.do?structureId=1j7a 2J7A.O]
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|-
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|Coverage
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| 68.3
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|-
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|E-value
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| 6e-11
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|}
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==Mutant 2==
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===NirS===
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[[File:DTU_NirS_NO.png|640px|center]]
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Figure 5: Nitrite reductase as a dimer with N<sub>2</sub> - source [http://www.rcsb.org/pdb/explore/explore.do?structureId=1nno 1NNO].
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===NirM===
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[[File:DTU_C551.png|640px|center]]
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Figure 6: Cytochrome c551 - source [http://www.rcsb.org/pdb/explore/explore.do?structureId=2exv 2EXV].
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===NOR===
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[[File:DTU_NOR.png|640px|center]]
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Figure 7: Flavorubredoxin - Homology model of NOR.
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{| class="wikitable"
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|-
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! style="background: silver" |Resource
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! style="background: #2B7C37" | NOR
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|-
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| Uniprot
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| [http://www.uniprot.org/uniprot/Q46877 Q46877]
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|-
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| Template pdb code and chain
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| [http://www.pdb.org/pdb/explore/explore.do?structureId=1ycf 1YCF.A]
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|-
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|Coverage
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| 82.5
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|-
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|E-value
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| 3e-95
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|}
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*All homology models were made using the free online tool [http://www.cbs.dtu.dk/services/CPHmodels/ CPHmodels v3.2]
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*All models were made and visualized in [http://sourceforge.net/projects/pymol/ PyMOL v1.6] which was easily compiled and installed using an [http://pymolwiki.org/index.php/User:Tlinnet/Linux_Install installation script] made by Troels Linnet.
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<div style="clear: both;"></div>
{{:Team:DTU-Denmark/Templates/EndPage}}
{{:Team:DTU-Denmark/Templates/EndPage}}

Latest revision as of 14:21, 3 October 2013

Protein Models

Contents

We have determined the structures of some proteins we want our mutants to express. Others could be homology modelled due to existing 3D models that had high similarity to the ones we are working with.

Mutant 1

AMO

DTU AMO.png

Figure 1: Ammonia monooxygenase (AMO). Homology models of all three subunits of AMO.

At the time of writing none of the three subunits from Nitrosomonas Europaea are available as 3D structures, so each of the subunits was identified at [http://www.uniprot.org/ UNIPROT], and their sequence was homology modelled using [http://www.cbs.dtu.dk/services/CPHmodels/ CPHmodels-3.2]

Resource AmoA AmoB AmoC
Uniprot [http://www.uniprot.org/uniprot/Q04507 Q04507] [http://www.uniprot.org/uniprot/Q04508 Q04508] [http://www.uniprot.org/uniprot/Q82T63 Q82T63]
Template pdb code and chain [http://www.pdb.org/pdb/explore/explore.do?structureId=1yew 1YEW.A] [http://www.pdb.org/pdb/explore/explore.do?structureId=1yew 1YEW.B] [http://www.pdb.org/pdb/explore/explore.do?structureId=3rgb 3RGB.C]
Coverage 90.5 86.2 66.4
E-value 1e-87 3e-67 8e-43

The three subunits were combined and aligned to the subunits of the [http://www.pdb.org/pdb/explore/explore.do?structureId=1yew Crystal structure] of particulate methane monooxygenase, hence an overlap of two alpha helices.

HAO

DTU Hao.png

Figure 2: Hydroxylamine oxidoreductase - source [http://www.rcsb.org/pdb/explore.do?structureId=1fgj 1FGJ].

Cc554

DTU CycA.png

Figure 3: Cytochrome c554 - source [http://www.rcsb.org/pdb/explore.do?structureId=1ft5 1FT5].

Ccm552

DTU Cycx.png


Figure 4: Homology model of Ccm552.


Resource Ccm552
Uniprot [http://www.uniprot.org/uniprot/Q50926 Q50926]
Template pdb code and chain [http://www.pdb.org/pdb/explore/explore.do?structureId=1j7a 2J7A.O]
Coverage 68.3
E-value 6e-11


Mutant 2

NirS

DTU NirS NO.png

Figure 5: Nitrite reductase as a dimer with N2 - source [http://www.rcsb.org/pdb/explore/explore.do?structureId=1nno 1NNO].

NirM

DTU C551.png

Figure 6: Cytochrome c551 - source [http://www.rcsb.org/pdb/explore/explore.do?structureId=2exv 2EXV].


NOR

DTU NOR.png

Figure 7: Flavorubredoxin - Homology model of NOR.


Resource NOR
Uniprot [http://www.uniprot.org/uniprot/Q46877 Q46877]
Template pdb code and chain [http://www.pdb.org/pdb/explore/explore.do?structureId=1ycf 1YCF.A]
Coverage 82.5
E-value 3e-95


  • All homology models were made using the free online tool [http://www.cbs.dtu.dk/services/CPHmodels/ CPHmodels v3.2]
  • All models were made and visualized in [http://sourceforge.net/projects/pymol/ PyMOL v1.6] which was easily compiled and installed using an [http://pymolwiki.org/index.php/User:Tlinnet/Linux_Install installation script] made by Troels Linnet.


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