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Penicillin-binding protein

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''E. coli'' PBP structure shows a distinct <scene name='47/478544/Cv/5'>3 domain structures</scene>. The <scene name='47/478544/Cv/6'>active site</scene> contains the <scene name='47/478544/Cv/7'>covalently bond between Ser62 and antibiotic ampicillin</scene><ref>PMID:16411754</ref>. Water molecules are shown as red spheres.
''E. coli'' PBP structure shows a distinct <scene name='47/478544/Cv/5'>3 domain structures</scene>. The <scene name='47/478544/Cv/6'>active site</scene> contains the <scene name='47/478544/Cv/7'>covalently bond between Ser62 and antibiotic ampicillin</scene><ref>PMID:16411754</ref>. Water molecules are shown as red spheres.
 +
 +
==3D structures of penicillin-binding protein==
 +
[[Penicillin-binding protein 3D structures]]
 +
</StructureSection>
</StructureSection>
==3D structures of penicillin-binding protein==
==3D structures of penicillin-binding protein==
Line 19: Line 23:
*'''Penicillin-binding protein'''
*'''Penicillin-binding protein'''
-
**[[1qme]], [[1rp5]], [[2z2l]] – SpPBP 2X – ''Streptococcus pneumoniae''<br />
+
**[[1qme]], [[1rp5]], [[2z2l]], [[5oau]] – SpPBP 2X – ''Streptococcus pneumoniae''<br />
**[[1k25]], [[1pyy]] – SpPBP 2X (mutant) <br />
**[[1k25]], [[1pyy]] – SpPBP 2X (mutant) <br />
**[[5u47]] - PBP 2X – ''Streptococcus thermophilus''<br />
**[[5u47]] - PBP 2X – ''Streptococcus thermophilus''<br />
Line 27: Line 31:
**[[2wad]], [[2wae]], [[2waf]] – SpPBP 2B<br />
**[[2wad]], [[2wae]], [[2waf]] – SpPBP 2B<br />
**[[3vma]] – EcPBP 1B - ''Escherichia coli''<br />
**[[3vma]] – EcPBP 1B - ''Escherichia coli''<br />
 +
**[[6g5r]], [[6fzk]] – EcPBP 1B UB2H domain – NMR<br />
**[[4bjp]] – EcPBP 3 residues 67-577<br />
**[[4bjp]] – EcPBP 3 residues 67-577<br />
**[[4bjq]] – EcPBP 3 residues 88-165<br />
**[[4bjq]] – EcPBP 3 residues 88-165<br />
Line 33: Line 38:
**[[1hd8]], [[1nj4]], [[1sdn]] – EcPBP 5 (mutant) <br />
**[[1hd8]], [[1nj4]], [[1sdn]] – EcPBP 5 (mutant) <br />
**[[3it9]] – EcPBP 6<br />
**[[3it9]] – EcPBP 6<br />
-
**[[1mwr]], [[1vqq]], [[4bl2]], [[4bl3]], [[4cpk]] - SaPBP 2A (mutant) – ''Staphylococcus aureus''<br />
+
**[[5tro]] - SaPBP 1 dimerization and transpeptidation domains – ''Staphylococcus aureus''<br />
-
**[[2olu]], [[3dwk]] – SaPBP 2<br />
+
**[[1mwr]], [[1vqq]], [[4bl2]], [[4bl3]], [[4cpk]] - SaPBP 2A (mutant) <br />
 +
**[[2olu]], [[3dwk]], [[5m1a]], [[5m19]], [[5m18]] – SaPBP 2<br />
**[[3vsk]] - SaPBP 3<br />
**[[3vsk]] - SaPBP 3<br />
**[[1tvf]] – SaPBP 4<br />
**[[1tvf]] – SaPBP 4<br />
 +
**[[6dz8]], [[6c3k]] – SaPBP 4 (mutant)<br />
**[[1w5d]] – BsPBP 4A – ''Bacillus subtilis''<br />
**[[1w5d]] – BsPBP 4A – ''Bacillus subtilis''<br />
**[[3mfd]] – BsPBP 5*<br />
**[[3mfd]] – BsPBP 5*<br />
**[[2oqo]] – AaPBP 1A – ''Aquifex aeolicus''<br />
**[[2oqo]] – AaPBP 1A – ''Aquifex aeolicus''<br />
**[[3equ]] – NgPBP 2 – ''Neisseria gonorrhoeae''<br />
**[[3equ]] – NgPBP 2 – ''Neisseria gonorrhoeae''<br />
-
**[[3eqv]] – NgPBP 2 (mutant) <br />
+
**[[3eqv]], [[5ksh]] – NgPBP 2 (mutant) <br />
-
**[[3a3d]] – HiPBP 4 – ''Haemophilus influenza''<br />
+
**[[6p52]], [[6p53]] – NgPBP 2 transpeptidase domain<br />
 +
**[[6p56]], [[4u3t]] – NgPBP 2 transpeptidase domain (mutant)<br />
 +
**[[5u2g]] – HiPBP 1A – ''Haemophilus influenza''<br />
 +
**[[3a3d]] – HiPBP 4 <br />
**[[3a3j]] – HiPBP 5<br />
**[[3a3j]] – HiPBP 5<br />
-
**[[3lo7]], [[3un7]] – MtPBP A – ''Mycobacterium tuberculosis''<br />
+
**[[3lo7]], [[3un7]], [[5crf]] – MtPBP A – ''Mycobacterium tuberculosis''<br />
-
**[[3oc2]], [[3pbn]] – PaPBP 3 – ''Pseudomonas aeruginosa''<br />
+
**[[3oc2]], [[3pbn]], [[6hr4]] – PaPBP 3 – ''Pseudomonas aeruginosa''<br />
**[[3tg9]] – PBP – ''Bacillus halodurans''<br />
**[[3tg9]] – PBP – ''Bacillus halodurans''<br />
**[[3udf]] – AbPBP – ''Acinetobacter baumannii''<br />
**[[3udf]] – AbPBP – ''Acinetobacter baumannii''<br />
**[[3zg7]] – LmPBP 4 – ''Listeria monocytogenes''<br />
**[[3zg7]] – LmPBP 4 – ''Listeria monocytogenes''<br />
-
**[[5dvy]], [[5e31]] – PBP 2 – ''Enterococcus faecium''<br />
+
**[[5dvy]], [[5e31]] – EfPBP 2 – ''Enterococcus faecium''<br />
 +
**[[6bsq]] - EfPBP 4<br />
 +
**[[6g0k]] - EfPBP 5 (mutant)<br />
 +
**[[5lp4]] – HpPBP 2 – ''Helicobacter pylor''i<br />
*Penicillin-binding protein complex with antibiotics
*Penicillin-binding protein complex with antibiotics
-
**[[1qmf]], [[2z2m]], [[2zc3]], [[2zc4]], [[2zc5]], [[2zc6]] – SpPBP 2X + antibiotic<br />
+
**[[1qmf]], [[2z2m]], [[2zc3]], [[2zc4]], [[2zc5]], [[2zc6]], [[5oj1]], [[5oj0]], [[5oiz]] – SpPBP 2X + antibiotic<br />
**[[1mwu]], [[1mwt]], [[1mws]] - SaPBP 2A (mutant) + antibiotic<br />
**[[1mwu]], [[1mwt]], [[1mws]] - SaPBP 2A (mutant) + antibiotic<br />
**[[2uwx]] - SaPBP 1B (mutant) + antibiotic<br />
**[[2uwx]] - SaPBP 1B (mutant) + antibiotic<br />
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**[[3zfz]], [[3zg0]], [[4dki]] - SaPBP 2’ + antibiotic<br />
**[[3zfz]], [[3zg0]], [[4dki]] - SaPBP 2’ + antibiotic<br />
**[[3vsl]] - SaPBP 3 + antibiotic<br />
**[[3vsl]] - SaPBP 3 + antibiotic<br />
-
**[[5txi]] - SaPBP 4 + antibiotic<br />
+
**[[5txi]], [[5ty7]], [[5tw8]] - SaPBP 4 + antibiotic<br />
-
**[[3hum]], [[3hun]] - SaPBP 4 (mutant) + antibiotic<br />
+
**[[3hum]], [[3hun]], [[5ty2]], [[5tx9]], [[5tw4]] - SaPBP 4 (mutant) + antibiotic<br />
**[[2c5w]] - SpPBP 1A + antibiotic<br />
**[[2c5w]] - SpPBP 1A + antibiotic<br />
**[[2jch]], [[2je5]], [[2xd1]] - SpPBP 1B (mutant) + antibiotic<br />
**[[2jch]], [[2je5]], [[2xd1]] - SpPBP 1B (mutant) + antibiotic<br />
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**[[3beb]], [[3bec]], [[3mzd]], [[3mze]], [[3mzf]] - EcPBP 5 + antibiotic<br />
**[[3beb]], [[3bec]], [[3mzd]], [[3mze]], [[3mzf]] - EcPBP 5 + antibiotic<br />
**[[3ita]] - EcPBP 6 + antibiotic<br />
**[[3ita]] - EcPBP 6 + antibiotic<br />
-
**[[3fwl]] – EcPBP 1B + antibiotic<br />
+
**[[3fwl]], [[5hld]], [[5hlb]], [[5hla]], [[5hl9]] – EcPBP 1B + antibiotic<br />
**[[3a3e]], [[3a3f]], [[3a3i]] – HiPBP 4 + antibiotic<br />
**[[3a3e]], [[3a3f]], [[3a3i]] – HiPBP 4 + antibiotic<br />
-
**[[3ocl]], [[3ocn]], [[3pbo]], [[3pbq]], [[3pbr]], [[3pbs]], [[3pbt]], [[4kqo]], [[4kqq]], [[4kqr]], [[4l0l]] – PaPBP 3 + antibiotic<br />
+
**[[4oon]] – PaPBP 1A + antibiotic<br />
 +
**[[3ocl]], [[3ocn]], [[3pbo]], [[3pbq]], [[3pbr]], [[3pbs]], [[3pbt]], [[4kqo]], [[4kqq]], [[4kqr]], [[4l0l]], [[6un1]], [[6hr6]] – PaPBP 3 + antibiotic<br />
 +
**[[6hr9]] – PaPBP 3 (mutant) + antibiotic<br />
**[[3nb6]], [[3nb7]] - AaPBP 1A + antibiotic<br />
**[[3nb6]], [[3nb7]] - AaPBP 1A + antibiotic<br />
**[[3udi]], [[3udx]], [[3ue0]], [[3ue1]] - AbPBP + antibiotic<br />
**[[3udi]], [[3udx]], [[3ue0]], [[3ue1]] - AbPBP + antibiotic<br />
 +
**[[3upn]], [[3upp]], [[5cxw]] - MtPBP A + antibiotic<br />
 +
**[[3upo]] - MtPBP A (mutant) + antibiotic<br />
 +
**[[3zg8]], [[3zg9]], [[3zga]] - LmPBP 4 + antibiotic<br />
 +
**[[6mkh]], [[6mki]], [[6bsr]] - EfPBP 4 + antibiotic<br />
 +
**[[6g88]] - EfPBP 5 + antibiotic<br />
 +
**[[6p54]], [[6p55]] – NgPBP 2 transpeptidase domain + antibiotic<br />
*Penicillin-binding protein complex with boronic acid derivatives
*Penicillin-binding protein complex with boronic acid derivatives
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*Penicillin-binding protein complex with other inhibitors
*Penicillin-binding protein complex with other inhibitors
-
**[[4fsf]] – PaPBP + inhibitor<br />
+
**[[4fsf]], [[4wel]], [[4wej]] - PaPBP 3 + inhibitor<br />
-
**[[4cjn]] – SaPBP + quinazolinine derivative<br />
+
**[[4wek]] – PaPBP 3 (mutant) + inhibitor<br />
 +
**[[5fgz]] – EcPBP 1B + inhibitor<br />
 +
**[[4cjn]] – SaPBP 2A + quinazolinine derivative<br />
 +
**[[6g9f]], [[6g9p]], [[6g9s]] – EcPBP 2 + inhibitor<br />
 +
**[[5lp5]] – HpPBP 2 + MREC <br />
 +
 
 +
*PBP D-alanyl-D-alanine carboxypeptidase or DD-transpeptidase
 +
 
 +
**[[1skf]] – StDADC - Streptomyces<br />
 +
**[[1es2]], [[1es3]], [[1es4]], [[1es5]], [[1esi]], [[1j9m]] – StDADC (mutant) <br />
 +
**[[1w79]], [[1w8q]], [[1w8y]] – AcDADC - Actinomadura<br />
 +
**[[2wke]], [[4ben]] – AcDADC + antibiotic <br />
 +
**[[2xk1]], [[2xln]], [[2y4a]], [[2y55]], [[2y59]], [[3zvt]], [[3zvw]], [[4b4x]], [[4b4z]] – AcDADC + boronic acid derivative <br />
 +
**[[2vgj]], [[2vgk]], [[2xdm]] – AcDADC + peptidoglycan analog <br />
 +
**[[3zcz]] – AcDADC + inhibitor <br />
 +
**[[4rye]] – MtDADC <br />
 +
**[[4ppr]] – MtDACB1 + antibiotic <br />
 +
**[[5fsr]] – EcDADC <br />
 +
**[[5j8x]] – EcDACA + boronic acid derivative <br />
 +
**[[6ntz]] – EcDADC + antibiotic <br />
 +
**[[6osu]] – DADC – ''Francisella tularensis'' <br />
}}
}}

Revision as of 08:30, 14 November 2019

E. coli PBP 4 complex with the antibiotic ampicillin and glycerol 2ex6

Drag the structure with the mouse to rotate

3D structures of penicillin-binding protein

Updated on 14-November-2019

References

  1. ↑ Spratt BG. Distinct penicillin binding proteins involved in the division, elongation, and shape of Escherichia coli K12. Proc Natl Acad Sci U S A. 1975 Aug;72(8):2999-3003. PMID:1103132
  2. ↑ Beadle BM, Nicholas RA, Shoichet BK. Interaction energies between beta-lactam antibiotics and E. coli penicillin-binding protein 5 by reversible thermal denaturation. Protein Sci. 2001 Jun;10(6):1254-9. PMID:11369864 doi:http://dx.doi.org/10.1110/ps.52001
  3. ↑ Kishida H, Unzai S, Roper DI, Lloyd A, Park SY, Tame JR. Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics. Biochemistry. 2006 Jan 24;45(3):783-92. PMID:16411754 doi:10.1021/bi051533t

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Michal Harel, Alexander Berchansky, Joel L. Sussman

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