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(-) Description

Title :  CRYSTAL STRUCTURE OF PBP2A FROM MRSA IN COMPLEX WITH PEPTIDOGLYCAN ANALOGUE AT ALLOSTERIC
 
Authors :  L. H. Otero, A. Rojas-Altuve, J. A. Hermoso
Date :  14 Dec 12  (Deposition) - 09 Oct 13  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Hydrolase, Penicillin Binding Proteins, 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 Plasmid: PET24D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Fragment: RESIDUES 27-668
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 158878
    Strain: STRAIN MU50
    Synonym: PENICILLIN-BINDING PROTEIN 2A
 
Molecule 2 - PEPTIDOGLYCAN ANALOGUE
    Chains: C, D
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1AMV2Mod. Amino AcidMETHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE
2CD4Ligand/IonCADMIUM ION
3CL4Ligand/IonCHLORIDE ION
4DAL4Mod. Amino AcidD-ALANINE
5FGA2Mod. Amino AcidGAMMA-D-GLUTAMIC ACID
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1AMV1Mod. Amino AcidMETHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE
2CD-1Ligand/IonCADMIUM ION
3CL-1Ligand/IonCHLORIDE ION
4DAL2Mod. Amino AcidD-ALANINE
5FGA1Mod. Amino AcidGAMMA-D-GLUTAMIC ACID
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1AMV1Mod. Amino AcidMETHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE
2CD-1Ligand/IonCADMIUM ION
3CL-1Ligand/IonCHLORIDE ION
4DAL2Mod. Amino AcidD-ALANINE
5FGA1Mod. Amino AcidGAMMA-D-GLUTAMIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:135 , HIS A:311 , CL A:1672 , ASP B:209BINDING SITE FOR RESIDUE CD A1669
02AC2SOFTWARETHR A:300 , CD A:1671BINDING SITE FOR RESIDUE CL A1670
03AC3SOFTWAREHIS A:143 , GLU A:145 , CL A:1670 , GLU B:145BINDING SITE FOR RESIDUE CD A1671
04AC4SOFTWAREGLU A:145 , HIS B:143 , GLU B:145 , CL B:1671BINDING SITE FOR RESIDUE CD B1669
05AC5SOFTWAREASP A:209 , GLY B:135 , GLN B:137 , HIS B:311 , CL B:1672BINDING SITE FOR RESIDUE CD B1670
06AC6SOFTWAREGLU A:145 , GLU B:145 , THR B:300 , VAL B:302 , CD B:1669BINDING SITE FOR RESIDUE CL B1671
07AC7SOFTWAREGLN A:207 , GLN B:137 , HIS B:311 , CD B:1670BINDING SITE FOR RESIDUE CL B1672
08AC8SOFTWAREGLN A:137 , GLN A:140 , HIS A:311 , CD A:1669 , GLN B:207BINDING SITE FOR RESIDUE CL A1672
09AC9SOFTWAREGLU A:150 , ARG A:151 , THR A:165 , LYS A:215 , THR A:216 , GLU A:239 , SER A:240 , ARG A:241 , VAL A:256 , PRO A:258 , VAL A:277 , HIS A:293 , MET A:372 , TYR A:373 , GLY A:374 , HOH A:2030 , HOH A:2053BINDING SITE FOR CHAIN C OF PEPTIDOGLYCAN ANALOGUE
10BC1SOFTWARELYS B:148 , ASN B:164 , THR B:165 , GLY B:166 , THR B:216 , GLU B:239 , SER B:240 , ARG B:241 , VAL B:256 , GLY B:257 , VAL B:277 , PHE B:371 , MET B:372 , TYR B:373 , GLY B:374 , MET B:375 , HOH B:2039 , HOH B:2060BINDING SITE FOR CHAIN D OF PEPTIDOGLYCAN ANALOGUE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZG5)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr A:363 -Pro A:364
2Lys B:219 -Met B:220
3Thr B:363 -Pro B:364
4Gly B:611 -Arg B:612
5Lys C:4 -Dal C:5
6Lys D:4 -Dal D:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZG5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZG5)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZG5)

(-) 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:636
 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 d3zg5a1 A:27-138 automated matches                                                                              d3zg5a2 A:139-327 automated matches                                                                                                                                                          d3zg5a3 A:328-668 automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeeeeeeee..eeeeeeeeeeeeee..eeeee.hhhhh.......eeeeeeee......ee.....eeeeeeeeeeeeehhhhhhhhhhhhhhhhhh.hhhhhhhhhh.........eeeeee......hhhhhhhhh.eeeeeeeee..hhhhhhhhhheeee.......hhhhh......eeeeehhhhhhhhhhh...eeeeeeee.....eeeeeeee.......ee...hhhhhhhhhhhhh...eeeeee......eeeeeee....hhhhhhh.hhhhhhhhhh...............hhhhhhhhhhhhhhhhh......eeee.......................eeeehhhhhhh.hhhhhhhhhhh.hhhhhhhhhhh...................hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...ee...........eee....hhhhhhhhhhhhhhhhhh............eeeeeeeee..------..eeeeeeeee......eeeeeee.......hhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zg5 A  27 DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLGKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELK------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  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           604    611                                                         


Chain B from PDB  Type:PROTEIN  Length:636
 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 d3zg5b1 B:27-138 automated matches                                                                              d3zg5b2 B:139-327 automated matches                                                                                                                                                          d3zg5b3 B:328-668 automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee.....eeeeeeeeee....eeeeeeeeeeeee..eeee..hhhhh.......eeeeeeee......ee.....eeeeeeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhh.........eeeeee......hhhhhhhh..eeeeeeeee..hhhhhhhhhh.eee..................eee.hhhhhhhhhhhh...eeeeeeee.....eeeeeeee.......ee...hhhhhhhhhhhhh...eeeeeee....eeeeeeee....hhhhhhh.hhhhhhhhhh...............hhhhhhhhhhhhhhhh.......eeee...ee..hhhhh...ee......eeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhh.......hhhhhhhhhhhhhh...ee...........eee....hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.....------...eeeeeeee......eeeeeee.......hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zg5 B  27 DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLGKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELK------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  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           604    611                                                         


Chain C from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3zg5 C   1 xAxKxx   6
                            | | ||
                            1-AMV|
                              3-FGA
                                5-DAL
                                 6-DAL


Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3zg5 D   1 xAxKxx   6
                            | | ||
                            | | ||
                            1-AMV|
                              3-FGA
                                5-DAL
                                 6-DAL
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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)

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 3ZG5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZG5)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3ZG5)

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  Cis Peptide Bonds
    Gly B:611 - Arg B:612   [ RasMol ]  
    Lys B:219 - Met B:220   [ RasMol ]  
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  3zg5
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  A0A0H3JPA5_S | A0A0H3JPA5
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  3.4.16.4
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 Related Entries

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

UniProtKB/TrEMBL
        A0A0H3JPA5_S | A0A0H3JPA5: 3zfz 3zg0 4bl2 4bl3 4cpk

(-) Related Entries Specified in the PDB File

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3zh3 CRYSTAL STRUCTURE OF S. PNEUMONIAE D39 NATIVE MURA1
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3zhg CRYSTALLOGRAPHIC STRUCTURE OF THE NATIVE MOUSE SIGN-R1 CRD DOMAIN