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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 COCRYSTALLIZATION
 
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 :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, 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
    Atcc700699
    ChainsA, B
    EC Number3.4.16.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantSTAR
    Expression System VectorPET24D
    Expression System Vector TypePLASMID
    FragmentRESIDUES 27-668
    Organism ScientificSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50
    Organism Taxid158878
    SynonymPENICILLIN-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, 18)

Asymmetric Unit (5, 18)
No.NameCountTypeFull Name
11W82Ligand/IonCEFTAROLINE
2AI82Ligand/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 (3, 3)
No.NameCountTypeFull Name
11W81Ligand/IonCEFTAROLINE
2AI81Ligand/IonCEFTAROLINE, BOUND FORM
3CD-1Ligand/IonCADMIUM ION
4CL-1Ligand/IonCHLORIDE ION
5MUR1Ligand/IonMURAMIC ACID

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:143 , GLU A:145 , ASN A:307 , CL A:1674 , GLU B:145BINDING SITE FOR RESIDUE CD A1670
02AC2SOFTWAREASP A:209 , HOH A:2083 , GLY B:135 , HIS B:311 , CL B:1675BINDING SITE FOR RESIDUE CD B1669
03AC3SOFTWAREHIS A:232BINDING SITE FOR RESIDUE CD A1671
04AC4SOFTWAREGLY A:135 , HIS A:311 , CL A:1675 , ASP B:209BINDING SITE FOR RESIDUE CD A1672
05AC5SOFTWAREASP A:320 , GLU B:150BINDING SITE FOR RESIDUE CD A1673
06AC6SOFTWAREGLU A:145 , THR A:300 , VAL A:302 , CD A:1670 , GLU B:145 , 1W8 B:1676BINDING SITE FOR RESIDUE CL A1674
07AC7SOFTWAREGLY A:135 , GLN A:137 , GLN A:140 , ALA A:310 , HIS A:311 , CD A:1672BINDING SITE FOR RESIDUE CL A1675
08AC8SOFTWAREGLU A:145 , HIS B:143 , GLU B:145 , CL B:1674BINDING SITE FOR RESIDUE CD B1671
09AC9SOFTWAREGLU A:59 , HIS B:232BINDING SITE FOR RESIDUE CD B1672
10BC1SOFTWAREASN B:569 , ASP B:573BINDING SITE FOR RESIDUE CD B1673
11BC2SOFTWARE1W8 A:1676 , HIS B:143 , GLU B:145 , THR B:300 , VAL B:302 , CD B:1671BINDING SITE FOR RESIDUE CL B1674
12BC3SOFTWAREGLN A:207 , GLY B:135 , GLN B:137 , HIS B:311 , CD B:1669BINDING SITE FOR RESIDUE CL B1675
13BC4SOFTWAREASN A:104 , TYR A:105 , ILE A:144 , GLU A:145 , ASN A:146 , GLU B:145 , ARG B:298 , SER B:306 , ASN B:307 , ILE B:309 , CL B:1674BINDING SITE FOR RESIDUE 1W8 A1676
14BC5SOFTWAREASN A:307 , ILE A:309 , CL A:1674 , ASN B:104 , TYR B:105 , ILE B:144 , TYR B:297BINDING SITE FOR RESIDUE 1W8 B1676
15BC6SOFTWAREGLU A:150 , ARG A:151 , THR A:165 , GLU A:239 , SER A:240 , ARG A:241 , VAL A:277 , HIS A:293 , HOH A:2067BINDING SITE FOR RESIDUE MUR A1677
16BC7SOFTWAREARG B:151 , THR B:165 , GLU B:239 , SER B:240 , ARG B:241 , VAL B:256 , VAL B:277 , GLN B:292 , HIS B:293BINDING SITE FOR RESIDUE MUR B1677
17BC8SOFTWAREGLY A:402 , SER A:403 , TYR A:446 , GLU A:447 , SER A:461 , SER A:462 , ASN A:464 , TYR A:519 , GLN A:521 , THR A:582 , SER A:598 , THR A:600 , ALA A:601 , GLU A:602 , ALA A:642 , HOH A:2168BINDING SITE FOR LIGAND AI8 A1403 BOUND TO SER A 403
18BC9SOFTWAREGLY B:402 , SER B:403 , TYR B:446 , SER B:462 , ASN B:464 , TYR B:519 , GLY B:520 , GLN B:521 , THR B:582 , HIS B:583 , ASP B:586 , SER B:598 , GLY B:599 , THR B:600 , ALA B:601 , GLU B:602 , ALA B:642 , SER B:643 , HOH B:2113 , HOH B:2156BINDING SITE FOR LIGAND AI8 B1403 BOUND TO SER B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZG0)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Thr A:363 -Pro A:364
2Gly A:608 -Glu A:609
3Thr B:363 -Pro B:364

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZG0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZG0)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZG0)

(-) 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: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 d3zg0a1 A:27-138 automated matches                                                                              d3zg0a2 A:139-327 automated matches                                                                                                                                                          d3zg0a3 A:328-668 automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeeeeeeeeeee..eeeeee..eeeee....eee..hhhhh.......eeeeeeee......ee.....eeeeeeeeeeeeehhhhhhhhhhhhhhhhhh.hhhhhhhhhh.........eeeeee...hhhhhhhhhhh..eeeeeeeee..hhhhhhhhhheeee.hhhhhhhhhhh......eeeeehhhhhhhhhhh...eeeeeeee....eeeeeeeee.......ee...hhhhhhhhhhh.....eeeeee......eeeeeee....hhhhhhh.hhhhhhhhhh...............hhhhhhhhhhhhhhhh........eee...ee..hhhhh...ee......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhh........hhhhhhhhhhhhh....ee...........eee....hhhhhhhhhhhhhhhhhh............eeeeeeeee..........eeeeeeeee......eeeeeee......hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zg0 A  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  

Chain B 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 d3zg0b1 B:27-138 automated matches                                                                              d3zg0b2 B:139-327 automated matches                                                                                                                                                          d3zg0b3 B:328-668 automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee..eeeeeeeeeeee..eeeeeeeeeeeee....eee..hhhhh.......eeeeeeee......ee.....eeeeeeeeeeeee.....hhhhhhhhhhhhh.hhhhhhhhhhh........eeeeee...hhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhheeee.......hhhhh......eeeeehhhhhhhhhhh...eeeeeeee.....eeeeeeee.......ee...hhhhhhhhhhh.....eeeeee......eeeeeee....hhhhhhh.hhhhhhhhhh...............hhhhhhhhhhhhhhhh........eee...ee..........ee......eeehhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...ee...........eee....hhhhhhhhhhhhhhhhhh.hhhhhh.....eeeee......-------..eeeeeeee......eeeeeee.......hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zg0 B  27 DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLGKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELK-------RQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 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  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           604     612                                                        

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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 6)

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        A0A0H3JPA5_S | A0A0H3JPA53zfz 3zg5 4bl2 4bl3 4cpk

(-) Related Entries Specified in the PDB File

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