7KIS

Crystal structure of Pseudomonas aeruginosa PBP2 in complex with WCK 5153


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural Characterization of Diazabicyclooctane beta-Lactam "Enhancers" in Complex with Penicillin-Binding Proteins PBP2 and PBP3 of Pseudomonas aeruginosa.

Rajavel, M.Kumar, V.Nguyen, H.Wyatt, J.Marshall, S.H.Papp-Wallace, K.M.Deshpande, P.Bhavsar, S.Yeole, R.Bhagwat, S.Patel, M.Bonomo, R.A.van den Akker, F.

(2021) mBio 12

  • DOI: 10.1128/mBio.03058-20
  • Primary Citation of Related Structures:  
    7KIS, 7KIT, 7KIV, 7KIW

  • PubMed Abstract: 
  • Multidrug-resistant (MDR) pathogens pose a significant public health threat. A major mechanism of resistance expressed by MDR pathogens is β-lactamase-mediated degradation of β-lactam antibiotics. The diazabicyclooctane (DBO) compounds zidebactam and WCK 5153, recognized as β-lactam "enhancers" due to inhibition of Pseudomonas aeruginosa penicillin-binding protein 2 (PBP2), are also class A and C β-lactamase inhibitors ...

    Multidrug-resistant (MDR) pathogens pose a significant public health threat. A major mechanism of resistance expressed by MDR pathogens is β-lactamase-mediated degradation of β-lactam antibiotics. The diazabicyclooctane (DBO) compounds zidebactam and WCK 5153, recognized as β-lactam "enhancers" due to inhibition of Pseudomonas aeruginosa penicillin-binding protein 2 (PBP2), are also class A and C β-lactamase inhibitors. To structurally probe their mode of PBP2 inhibition as well as investigate why P. aeruginosa PBP2 is less susceptible to inhibition by β-lactam antibiotics compared to the Escherichia coli PBP2, we determined the crystal structure of P. aeruginosa PBP2 in complex with WCK 5153. WCK 5153 forms an inhibitory covalent bond with the catalytic S327 of PBP2. The structure suggests a significant role for the diacylhydrazide moiety of WCK 5153 in interacting with the aspartate in the S-X-N/D PBP motif. Modeling of zidebactam in the active site of PBP2 reveals a similar binding mode. Both DBOs increase the melting temperature of PBP2, affirming their stabilizing interactions. To aid in the design of DBOs that can inhibit multiple PBPs, the ability of three DBOs to interact with P. aeruginosa PBP3 was explored crystallographically. Even though the DBOs show covalent binding to PBP3, they destabilized PBP3. Overall, the studies provide insights into zidebactam and WCK 5153 inhibition of PBP2 compared to their inhibition of PBP3 and the evolutionarily related KPC-2 β-lactamase. These molecular insights into the dual-target DBOs advance our knowledge regarding further DBO optimization efforts to develop novel potent β-lactamase-resistant, non-β-lactam PBP inhibitors. IMPORTANCE Antibiotic resistance is a significant clinical problem. Developing novel antibiotics that overcome known resistance mechanisms is highly desired. Diazabicyclooctane inhibitors such as zidebactam possess this potential as they readily inactivate penicillin-binding proteins, yet cannot be degraded by β-lactamases. In this study, we characterized the inhibition by diazabicyclooctanes of penicillin-binding proteins PBP2 and PBP3 from Pseudomonas aeruginosa using protein crystallography and biophysical analyses. These structures and analyses help define the antibiotic properties of these inhibitors, explain the decreased susceptibility of P. aeruginosa PBP2 to be inhibited by β-lactam antibiotics, and provide insights that could be used for further antibiotic development.


    Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, USA focco.vandenakker@case.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidoglycan D,D-transpeptidase MrdAA, B646Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
pbpAmrdApenAspoVDCAZ10_26315CGU42_07245E4V10_04960E5D53_29900E5Z62_22855E5Z63_21270ECC04_009785GNQ48_15490GUL26_00100IPC111_26370IPC112_16150IPC113_04200IPC114_13770IPC115_04200IPC116_28685IPC117_22480IPC118_29205IPC119_28570IPC120_28740IPC121_28940IPC122_18400IPC123_09075IPC124_23345IPC125_20245IPC126_16605IPC127_00100IPC128_01080IPC1295_14660IPC129_04675IPC1306_14480IPC1307_21080IPC1308_11685IPC1309_25910IPC130_01080IPC1311_00100IPC1312_20590IPC1314_12785IPC1315_04205IPC1316_16175IPC1317_16140IPC1318_05355IPC1319_19340IPC131_20795IPC1320_14575IPC1321_05595IPC1322_04255IPC1323_04255IPC1324_04255IPC1325_17515IPC1326_21135IPC1327_21115IPC1328_04220IPC1329_19725IPC132_23085IPC1330_04265IPC1331_21980IPC1332_04570IPC1333_18255IPC1336_27775IPC1337_21965IPC1339_04380IPC1340_08930IPC1341_04400IPC1342_07510IPC1343_04490IPC1348_25965IPC1349_28390IPC134_20870IPC137_31680IPC139_11735IPC140_14650IPC141_19090IPC142_19215IPC143_16785IPC144_04975IPC145_28050IPC146_22890IPC1474_12170IPC1476_31580IPC1477_18495IPC1478_32240IPC1479_21185IPC147_18095IPC1480_13520IPC1481_15245IPC1482_24180IPC1485_05030IPC1486_06710IPC1487_06215IPC1489_03020IPC148_29060IPC1490_07875IPC1491_17395IPC1492_14930IPC1494_08120IPC1495_27085IPC1496_32010IPC1498_08625IPC1499_24670IPC149_28740IPC1500_17680IPC1501_19400IPC1502_29675IPC1503_07525IPC1504_30160IPC1505_11120IPC1506_25340IPC1507_20970IPC1508_04685IPC1509_03715IPC150_03845IPC1510_30175IPC1511_07090IPC1512_10455IPC1513_04235IPC1514_08805IPC1515_29100IPC1516_22610IPC1517_19445IPC1518_19250IPC1519_04515IPC151_03845IPC1521_04600IPC1522_25770IPC1523_07925IPC152_05870IPC153_14040IPC154_14845IPC155_11125IPC156_16980IPC157_04520IPC1583_04205IPC1584_23125IPC1585_10005IPC1586_22865IPC1587_10360IPC1588_24795IPC1589_19050IPC158_19910IPC1591_06775IPC1592_26210IPC1594_25435IPC1595_08945IPC1596_00100IPC1597_00100IPC1598_32125IPC1599_08415IPC159_14780IPC1600_26600IPC1601_03225IPC1602_21180IPC1603_26265IPC1604_13815IPC1605_21950IPC1606_16690IPC161_20160IPC162_29785IPC163_09360IPC164_30715IPC165_09365IPC166_29220IPC167_29370IPC168_05740IPC169_09360IPC170_30060IPC171_29545IPC172_08865IPC173_10605IPC174_15160IPC175_03220IPC176_10360IPC177_27825IPC178_19040IPC179_18860IPC180_21070IPC181_23770IPC182_28845IPC183_19870IPC184_14380IPC27_27490IPC29_24820IPC30_08995IPC31_24160IPC32_21845IPC33_11915IPC34_20260IPC35_20430IPC36_22320IPC37_06550IPC38_00100IPC41_05230IPC42_09200IPC43_12010IPC44_08575IPC45_24755IPC46_17410IPC47_18460IPC48_25905IPC49_18835IPC50_15005IPC51_11720IPC54_14245IPC55_11610IPC56_07395IPC574_30560IPC575_30765IPC576_25825IPC577_27695IPC578_30680IPC579_30655IPC57_26020IPC580_30620IPC582_30450IPC584_30310IPC586_25865IPC589_30580IPC58_05760IPC596_06965IPC597_13880IPC598_04620IPC599_06965IPC59_06925IPC600_06970IPC601_06960IPC602_06970IPC603_12835IPC604_23185IPC605_24365IPC606_26490IPC607_03590IPC608_12915IPC609_19795IPC60_10770IPC610_11565IPC611_30245IPC612_27705IPC613_31445IPC614_24340IPC615_27300IPC616_27195IPC618_28685IPC61_26385IPC620_24725IPC621_10850IPC622_06965IPC623_04495IPC624_21890IPC625_26900IPC627_28300IPC629_07085IPC630_14035IPC632_10885IPC633_19155IPC634_17620IPC65_22995IPC66_16695IPC67_19840IPC68_15430IPC70_01095IPC71_03225IPC72_06770IPC737_17705IPC73_31090IPC74_26355IPC75_20440IPC76_20440IPC77_10420IPC78_18405NCTC13621_06836PA52Ts2_5394

EC: 3.4.16.4
UniProt
Find proteins for Q9X6V3 (Pseudomonas aeruginosa)
Explore Q9X6V3 
Go to UniProtKB:  Q9X6V3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X6V3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C9D (Subject of Investigation/LOI)
Query on C9D

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
(2S,5R)-1-formyl-N'-[(3R)-pyrrolidine-3-carbonyl]-5-[(sulfooxy)amino]piperidine-2-carbohydrazide
C12 H21 N5 O7 S
MPNPDELHXLJIKQ-BBBLOLIVSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.018α = 90
b = 75.924β = 106.73
c = 97.299γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references