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==5YPI Mechanism of NDM-1==
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==Your Heading Here (maybe something like 'Structure')==
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<StructureSection load='5YPI' size='340' side='right' caption='Caption for this structure' scene='/78/781194/5ypi-1/1'>
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<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
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The 5YPI structure of NDM-1 contains 14,682 atoms, 14,184 bonds, 2729 groups, and 8 chains.
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This is a default text for your page '''Sandbox GGC8'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
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New Delhi metallo-beta-lactamases (NDMs), pose a serious threat due to their extremely efficient mechanism of hydrolysis on beta-lactam antibiotics. These antibiotics target the penicillin-binding proteins in enzymes found anchored in the cell membrane, which are involved in the cross-linking of the bacterial cell wall. The beta-lactam ring binds to different penicillin-binding proteins making them unable to do cell wall synthesis which leads to death of the bacterial cell. The NDM-1 gene causes the bacterium to produce an enzyme that neutralizes even the strongest antibiotic family: (Carbapenems)and only used as last resort. The bacteria strain that carries the NDM-1 gene are so dangerous because we have very few ways to fight them. Metallo-beta-lactamases-mediated hydrolysis happens in two steps: cleavage of the amide bond and protonation of the generated intermediate .After the formation of a Michaels complex (ES), a water/hydroxide molecule residing between the two Zn(II) ions acts as a nucleophile to attack the carbonyl carbon (C7) and cleave the C–N bond next the intermediate is protonated, and an EP complex is tentatively formed before product is release from the enzyme pocket, this was first detected in a Klebsiella pneumoniae case in India (hence the name)in 2009.My paper" The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis" explores the mechanism reaction of New Delhi metallo-beta-lactamases using NMR and crystallography, the hydrolysis of three enzyme-intermediates are examined, EI1, EI2, and EP, The data suggested that the hydrolytic intermediates are protonated by a bulky water molecule incoming from the β-face. This research is important because it could help provide a design model for mechanism-based inhibitors.
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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.
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The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis
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== Function ==
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Han Feng, Xuehui Liu, Sheng Wang, Joy Fleming, Da-Cheng Wang & Wei Liu
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== Function == Hydrolase
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== Disease ==
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== Disease == New Delhi metallo-beta-lactamase 1 is an enzyme that makes bacteria resistant to a broad range of beta-lactam antibiotics.
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== Relevance ==
== Structural highlights ==
== Structural highlights ==
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<scene name='78/781194/Secondary_structure/2'>Secondary Structure</scene> This scene shows the different secondary structures color-coded.
 
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<scene name='78/781194/Secondary_structure_2/1'>secondary structure 2</scene>
 
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{{Template:ColorKey_Helix}},
 
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{{Template:ColorKey_Strand}},
 
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{{Template:ColorKey_Loop}},
 
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{{Template:ColorKey_Turn}}.
 
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<scene name='78/781194/Composition/1'>Composition</scene> This scene shows the Protein, solvent, and ligand sites color coded below.
 
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{{Template:ColorKey Composition Protein}}
 
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{{Template:ColorKey Composition Ligand}}
 
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{{Template:ColorKey Composition Solvent}}
 
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<scene name='78/781194/Elements/1'>Elements</scene> This scene shows the different elements color coded.
 
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{{Template:ColorKey_Element_C}}
 
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{{Template:ColorKey_Element_H}}
 
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{{Template:ColorKey_Element_O}}
 
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{{Template:ColorKey_Element_N}}
 
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{{Template:ColorKey_Element_P}}
 
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{{Template:ColorKey_Element_S}}
 
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{{Template:ColorKey_Element_Se}}
 
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{{Template:ColorKey_Element_Fe}}
 
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<scene name='78/781194/8chains/2'>Chains</scene> This scene shows the 8 chains linked together.
 
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<scene name='78/781194/Zn_pairs/1'>Zn Pairs</scene> This scene shows the 8 Zn pairs(one for each chain).
 
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<scene name='78/781194/5ypi_elements_only/1'>elements-only</scene> This scene shows a view of the molecules without the secondary structures.
 
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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>
</StructureSection>
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== References ==
== References ==
<references/>
<references/>
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https://www.nature.com/articles/s41467-017-02339-w
 
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https://rdcu.be/MgiZ
 

Revision as of 22:28, 17 September 2019

Your Heading Here (maybe something like 'Structure')

Caption for this structure

Drag the structure with the mouse to rotate

References

  1. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
  2. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
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