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(-) Description

Title :  CRYSTAL STRUCTURE OF PBP2A CLINICAL MUTANT N146K FROM MRSA
 
Authors :  L. H. Otero, A. Rojas-Altuve, C. Carrasco-Lopez, J. A. Hermoso
Date :  30 Apr 13  (Deposition) - 21 May 14  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
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 :  J. Fishovitz, A. Rojas-Altuve, L. H. Otero, M. Dawley, C. Carrasco-Lopez, M. Chang, J. A. Hermoso, S. Mobashery
Disruption Of Allosteric Response As An Unprecedented Mechanism Of Resistance To Antibiotics.
J. Am. Chem. Soc. V. 136 9814 2014
PubMed-ID: 24955778  |  Reference-DOI: 10.1021/JA5030657

(-) 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 26-668
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: MU50
    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  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1CD7Ligand/IonCADMIUM ION
2CL4Ligand/IonCHLORIDE ION
3MUR2Ligand/IonMURAMIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MUR1Ligand/IonMURAMIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MUR1Ligand/IonMURAMIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:143 , GLU A:145 , CL A:1010 , GLU B:145BINDING SITE FOR RESIDUE CD A 1001
02AC2SOFTWAREASP A:209 , GLY B:135 , HIS B:311 , CL B:1012BINDING SITE FOR RESIDUE CD A 1003
03AC3SOFTWAREHIS A:232 , GLU B:378BINDING SITE FOR RESIDUE CD A 1004
04AC4SOFTWAREGLY A:135 , HIS A:311 , CL A:1011 , ASP B:209BINDING SITE FOR RESIDUE CD A 1005
05AC5SOFTWAREHIS A:143 , GLU A:145 , THR A:300 , CD A:1001 , GLU B:145BINDING SITE FOR RESIDUE CL A 1010
06AC6SOFTWAREGLN A:137 , HIS A:311 , CD A:1005 , GLN B:207BINDING SITE FOR RESIDUE CL A 1011
07AC7SOFTWAREARG A:151 , ASN A:164 , THR A:165 , GLU A:239 , SER A:240 , ARG A:241 , VAL A:277 , HIS A:293BINDING SITE FOR RESIDUE MUR A 1677
08AC8SOFTWAREGLU A:145 , HIS B:143 , GLU B:145 , CL B:1009BINDING SITE FOR RESIDUE CD B 1002
09AC9SOFTWAREGLU A:59 , HIS B:232BINDING SITE FOR RESIDUE CD B 1006
10BC1SOFTWAREASN B:569 , ASP B:573BINDING SITE FOR RESIDUE CD B 1007
11BC2SOFTWAREGLU A:145 , THR B:300 , ILE B:309 , CD B:1002BINDING SITE FOR RESIDUE CL B 1009
12BC3SOFTWARECD A:1003 , GLY B:135 , HIS B:311BINDING SITE FOR RESIDUE CL B 1012
13BC4SOFTWAREGLU B:150 , ARG B:151 , ASN B:164 , THR B:165 , GLU B:239 , SER B:240 , ARG B:241 , VAL B:277 , GLN B:292 , HIS B:293BINDING SITE FOR RESIDUE MUR B 1677

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BL3)

(-) 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 4BL3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BL3)

(-) Exons   (0, 0)

(no "Exon" information available for 4BL3)

(-) 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:640
 aligned with A0A0H3JPA5_S | A0A0H3JPA5 from UniProtKB/TrEMBL  Length:668

    Alignment length:643
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665   
         A0A0H3JPA5_S    26 KDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLGKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 668
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee..eeeeeeeeeee....eeeee..eeeee....eee..hhhhh.......eeeeeeee......ee.....eeeeeeeeeeeeehhhhhhhhhhhhhhhhhh.hhhhhhhhhh.........eeeeee....hhhhhhhhhhh.eeeeeeeee..hhhhhh....eeee.hhhhhhhhhhh......eeeeehhhhhhhhhhh...eeeeeeee....eeeeeeeee.......ee...hhhhhhhhhhh....eeeeeeee....eeeeeeee....hhhhhh..hhhhhhhhhhh..............hhhhhhhhhhhhhhhh.......eeee...ee..........ee......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhh........hhhhhhhhhhhhhh...ee...........eee....hhhhhhhhhhhhhhhhhh............eeeeee........---...eeeeeeee......eeeeeee......hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bl3 A  26 KDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIEKLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLGKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQ---GRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 668
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605 |   | 615       625       635       645       655       665   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               607 611                                                         


Chain B from PDB  Type:PROTEIN  Length:639
 aligned with A0A0H3JPA5_S | A0A0H3JPA5 from UniProtKB/TrEMBL  Length:668

    Alignment length:643
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665   
         A0A0H3JPA5_S    26 KDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLGKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 668
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee..eeeeeeeeeee....eeeeeeeeeeeee..eeee..hhhhh.......eeeeeeee......ee.....eeeeeeeeeeeee.....hhhhhhhhhhhhh.hhhhhhhhhh.........eeeeee...hhhhhhhhhhh..eeeeeeeee..hhhhhh....eeee...hhhhh..........eeeeehhhhhhhhhhh...eeeeeeee....eeeeeeeee.......ee...hhhhhhhhhhhhh..eeeeeee......eeeeeee....hhhhhh..hhhhhhhhhh.................hhhhhhhhhhhhhh.......eeee...ee..........ee......eeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhh........hhhhhhhhhhhhhh...ee...........eee....hhhhhhhhhhhhhhhhhh............eeee.........----...eeeeeeee......eeeeeee.......hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bl3 B  26 KDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIEKLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLGKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMK----GRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 668
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605|    | 615       625       635       645       655       665   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              606  611
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4BL3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BL3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BL3)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4BL3)

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 Related Entries

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

UniProtKB/TrEMBL
        A0A0H3JPA5_S | A0A0H3JPA5: 3zfz 3zg0 3zg5 4bl2 4cpk

(-) Related Entries Specified in the PDB File

4bl2 CRYSTAL STRUCTURE OF PBP2A CLINICAL MUTANT E150K FROM MRSA