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(-) Description

Title :  CRYSTAL STRUCTURE OF CEFTAROLINE ACYL-PBP2A FROM MRSA WITH NON-COVALENTLY BOUND CEFTAROLINE AND MURAMIC ACID AT ALLOSTERIC SITE OBTAINED BY SOAKING
 
Authors :  L. H. Otero, A. Rojas-Altuve, J. A. Hermoso
Date :  13 Dec 12  (Deposition) - 09 Oct 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Penicillin Binding Proteins, Mrsa, Allosteric Site, B- Lactam Antibiotics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. H. Otero, A. Rojas-Altuve, L. I. Llarrull, C. Carrasco-Lopez, M. Kumarasiri, E. Lastochkin, J. Fishovitz, M. Dawley, D. Hesek, M. Lee, J. W. Johnson, J. F. Fisher, M. Chang, S. Mobashery, J. A. Hermos
How Allosteric Control Of Staphylococcus Aureus Penicillin Binding Protein 2A Enables Methicillin Resistance And Physiological Function
Proc. Natl. Acad. Sci. Usa V. 110 16808 2013
PubMed-ID: 24085846  |  Reference-DOI: 10.1073/PNAS.1300118110

(-) Compounds

Molecule 1 - PENICILLIN BINDING PROTEIN 2 PRIME
    Atcc: 700699
    Chains: A, B
    EC Number: 3.4.16.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector: PET24D
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 27-668
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50
    Organism Taxid: 158878
    Synonym: PENICILLIN-BINDING PROTEIN 2A

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
11W81Ligand/IonCEFTAROLINE
2AI81Ligand/IonCEFTAROLINE, BOUND FORM
3CD8Ligand/IonCADMIUM ION
4CL4Ligand/IonCHLORIDE ION
5MUR2Ligand/IonMURAMIC ACID
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
11W81Ligand/IonCEFTAROLINE
2AI81Ligand/IonCEFTAROLINE, BOUND FORM
3CD-1Ligand/IonCADMIUM ION
4CL-1Ligand/IonCHLORIDE ION
5MUR1Ligand/IonMURAMIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11W8-1Ligand/IonCEFTAROLINE
2AI8-1Ligand/IonCEFTAROLINE, BOUND FORM
3CD-1Ligand/IonCADMIUM ION
4CL-1Ligand/IonCHLORIDE ION
5MUR1Ligand/IonMURAMIC ACID

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:143 , GLU A:145 , CL A:1010 , GLU B:145BINDING SITE FOR RESIDUE CD A1001
02AC2SOFTWAREASP A:209 , GLY B:135 , HIS B:311 , CL B:1012BINDING SITE FOR RESIDUE CD A1003
03AC3SOFTWAREHIS A:232 , GLU B:378 , GLU B:385BINDING SITE FOR RESIDUE CD A1004
04AC4SOFTWAREGLY A:135 , HIS A:311 , CL A:1011 , HOH A:2051 , ASP B:209BINDING SITE FOR RESIDUE CD A1005
05AC5SOFTWAREASP A:320 , GLU B:150BINDING SITE FOR RESIDUE CD A1008
06AC6SOFTWAREGLU A:145 , THR A:300 , CD A:1001 , GLU B:145BINDING SITE FOR RESIDUE CL A1010
07AC7SOFTWAREGLY A:135 , GLN A:137 , GLN A:140 , HIS A:311 , CD A:1005 , GLN B:207BINDING SITE FOR RESIDUE CL A1011
08AC8SOFTWAREGLU A:145 , HOH A:2057 , HIS B:143 , GLU B:145 , CL B:1009BINDING SITE FOR RESIDUE CD B1002
09AC9SOFTWAREGLU A:59 , HIS B:232BINDING SITE FOR RESIDUE CD B1006
10BC1SOFTWAREASN B:569 , ASP B:573 , HOH B:2257BINDING SITE FOR RESIDUE CD B1007
11BC2SOFTWARE1W8 A:1669 , GLU B:145 , THR B:300 , VAL B:302 , CD B:1002BINDING SITE FOR RESIDUE CL B1009
12BC3SOFTWAREGLN A:207 , CD A:1003 , GLY B:135 , GLN B:140 , HIS B:311BINDING SITE FOR RESIDUE CL B1012
13BC4SOFTWAREASN A:104 , TYR A:105 , ILE A:144 , GLU A:145 , ASN A:146 , ASP A:275 , HOH A:2038 , HOH A:2059 , GLU B:145 , ASN B:146 , LEU B:147 , ARG B:298 , SER B:306 , ASN B:307 , CL B:1009BINDING SITE FOR RESIDUE 1W8 A1669
14BC5SOFTWAREGLU A:150 , ARG A:151 , THR A:165 , GLU A:239 , SER A:240 , ARG A:241 , VAL A:256 , VAL A:277 , MET A:372 , HOH A:2065 , HOH A:2080BINDING SITE FOR RESIDUE MUR A1670
15BC6SOFTWAREGLU B:150 , ARG B:151 , THR B:165 , GLU B:239 , SER B:240 , ARG B:241 , VAL B:256 , VAL B:277 , MET B:372 , HOH B:2128BINDING SITE FOR RESIDUE MUR B1669
16BC7SOFTWAREGLY A:402 , SER A:403 , LYS A:406 , TYR A:446 , SER A:461 , SER A:462 , ASN A:464 , TYR A:519 , GLY A:520 , GLN A:521 , THR A:582 , LYS A:597 , SER A:598 , THR A:600 , ALA A:601 , GLU A:602 , HOH A:2219 , HOH A:2323BINDING SITE FOR LIGAND AI8 A1403 BOUND TO SER A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZFZ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:363 -Pro A:364
2Thr B:363 -Pro B:364

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZFZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZFZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZFZ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:635
 aligned with A0A0H3JPA5_S | A0A0H3JPA5 from UniProtKB/TrEMBL  Length:668

    Alignment length:642
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666  
         A0A0H3JPA5_S    27 DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLGKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 668
               SCOP domains d3zfza1 A:27-138 automated matches                                                                              d3zfza2 A:139-327 automated matches                                                                                                                                                          d3zfza3 A:328-668 automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee..eeeeeeeeeeee..eeeeeeeeeeeee....eeee.hhhhh.......eeeeeeee......ee.....eeeeeeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhh.........eeeeee......hhhhhhhh..eeeeeeeee..hhhhhhhhhh.eee.......hhhhh......eee.hhhhhhhhhhhh...eeeeeeee.....eeeeeeee.......ee...hhhhhhhhhhh....eeeeeee......eeeeeee....hhhhhhh.hhhhhhhhhh..................hhhhhhhhhhhhh.......eeee...ee..hhhhh...ee......eeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhh........hhhhhhhhhhhhhh...ee...........eee....hhhhhhhhhhhhhhhhhh............eeeeeeee..-------...eeeeeeee..eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zfz A  27 DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLGKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAEL-------GRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 668
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596      |  -    |  616       626       636       646       656       666  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          603     611                                                         


Chain B from PDB  Type:PROTEIN  Length:642
 aligned with A0A0H3JPA5_S | A0A0H3JPA5 from UniProtKB/TrEMBL  Length:668

    Alignment length:642
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666  
         A0A0H3JPA5_S    27 DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLGKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 668
               SCOP domains d3zfzb1 B:27-138 automated matches                                                                              d3zfzb2 B:139-327 automated matches                                                                                                                                                          d3zfzb3 B:328-668 automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeeeeeeeeeee..eeeeeeeeeeeeee..eeee..hhhhh.......eeeeeeee......ee.....eeeeeeeeeeeee........hhhhhhhhh..hhhhhhhhhhh........eeeeee...hhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhh.eee...hhhhh..........eee.hhhhhhhhhhhh...eeeeeeee.....eeeeeeee.......ee...hhhhhhhhhhhhh..eeeeeee......eeeeeee....hhhhhhh.hhhhhhhhhh...............hhhhhhhhhhhhhhhh.......eeee...ee..hhhhh...ee......eeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhh.......hhhhhhhhhhhhhh...ee...........eee....hhhhhhhhhhhhhhhhhh............eeee..eee..........eeeeeeeee......eeeeeee.......hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zfz B  27 DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLGKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 668
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZFZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZFZ)

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Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3ZFZ)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        A0A0H3JPA5_S | A0A0H3JPA5: 3zg0 3zg5 4bl2 4bl3 4cpk

(-) Related Entries Specified in the PDB File

3zg0 CRYSTAL STRUCTURE OF CEFTAROLINE ACYL-PBP2A FROM MRSA WITH NON-COVALENTLY BOUND CEFTAROLINE AND MURAMIC ACID AT ALLOSTERIC SITE OBTAINED BY COCRYSTALLIZATION
3zg5 CRYSTAL STRUCTURE OF PBP2A FROM MRSA IN COMPLEX WITH PEPTIDOGLYCAN ANALOGUE AT ALLOSTERIC