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(-) Description

Title :  CRYSTAL STRUCTURE OF PENICILLIN BINDING PROTEIN 4 FROM LISTERIA MONOCYTOGENES IN THE AMPICILLIN BOUND FORM
 
Authors :  J. H. Jeong, Y. G. Kim
Date :  17 Dec 12  (Deposition) - 29 May 13  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Penicillin-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jeong, Y. Kim, C. Rojviriya, S. Ha, B. S. Kang, Y. Kim
Crystal Structures Of Bifunctional Penicillin-Binding Protein 4 From Listeria Monocytogenes.
Antimicrob. Agents Chemother. V. 57 3507 2013
PubMed-ID: 23669378  |  Reference-DOI: 10.1128/AAC.00144-13

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEXHTA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 73-119
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 1639
    Other Details: PROTEOLYSIS FROM 120-177
    Synonym: LMO2229 PROTEIN
 
Molecule 2 - PENICILLIN-BINDING PROTEIN 4
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEXHTA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 178-714
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 1639
    Synonym: LMO2229 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1AIX1Ligand/Ion(2R,4S)-2-[(1R)-1-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}-2-OXOETHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2GOL3Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:427 , LEU B:488 , THR B:579 , GLN B:580 , AIX B:800 , HOH B:2083BINDING SITE FOR RESIDUE GOL B1643
2AC2SOFTWAREALA B:347 , ASN B:348 , GLU B:615 , HIS B:616 , TYR B:617BINDING SITE FOR RESIDUE GOL B1644
3AC3SOFTWARELYS B:389 , ALA B:390 , GLN B:391 , LYS B:590 , ASP B:591 , HOH B:2108BINDING SITE FOR RESIDUE GOL B1645
4AC4SOFTWAREGLY B:393 , SER B:394 , VAL B:432 , SER B:449 , ASN B:451 , THR B:576 , SER B:578 , GLN B:580 , THR B:589 , SER B:623 , GOL B:1643 , HOH B:2084BINDING SITE FOR LIGAND AIX B 800 BOUND TO SER B 394

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZG8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZG8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZG8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZG8)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZG8)

(-) Sequences/Alignments

Asymmetric/Biological 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:39
 aligned with Q8Y547_LISMO | Q8Y547 from UniProtKB/TrEMBL  Length:714

    Alignment length:39
                                    86        96       106         
         Q8Y547_LISMO    77 ATIIYDKDGDKAGELSSTDATFVSIDKISKNLQNAVVSI 115
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeee........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 3zg8 A  77 ATIIYDKDGDKAGELSSTDATFVSIDKISKNLQNAVVSI 115
                                    86        96       106         


Chain B from PDB  Type:PROTEIN  Length:458
 aligned with Q8Y547_LISMO | Q8Y547 from UniProtKB/TrEMBL  Length:714

    Alignment length:458
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633        
         Q8Y547_LISMO   184 YSKDEIMEMYLNRSYFGNGEWGVENASLKYFGKSAADLNIPEAATIAGLLQAPSAYDPYQHIDKATNRRNMVLNAMVETGTISKAEGDKYKATKIVLNDQSKDPLANKYPWYVDAVINEAVNEADITQDEIMQKGYKIYTELDQNYQTSLENVYNNDGLFPSNANDGTLVQSGAVLMDPATGGIRALVGGRGEHVFRGFNRATQMKAQPGSTMKPLAVYTPALQSGYDVDSMLKDEKITYKGNYTPTNVGGVYSGEVPMYKAVANSINAPAVWLLDQIGIDKGVKSVEKFGITVPEKDRTLGLALGGMSKGASPVEMATAYATFANNGAKPESHIITKIVDPSGNTVYENVPKTKQIISETVSNEMTSMLLDVINTGTGQSAAVSGHEMAGKTGSTQVPFDDTSGTKDQWFVGYTPNLVGAVWMGYDKTDKEHYLTTTSSAGVSSLAHYVMNSGLQYQ 641
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...............hhhhhhhhhhhhhhhh..hhhhhhhh..eeee..hhhhhhhhhhhhhhhhhh..........eeeeeeee....eeeeee....................hhhhhhhhhhhhhhhhh......eeee.....hhh...........eeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhhhhh..ee.....eeeee.....eeee.....ee..hhhhhhhhhhhhhhhhhhh.hhhhh......eeeeeeee........eeeeeeeeee..eeeeeeee..............hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zg8 B 184 YSKDEIMEMYLNRSYFGNGEWGVENASLKYFGKSAADLNIPEAATIAGLLQAPSAYDPYQHIDKATNRRNMVLNAMVETGTISKAEGDKYKATKIVLNDQSKDPLANKYPWYVDAVINEAVNEADITQDEIMQKGYKIYTELDQNYQTSLENVYNNDGLFPSNANDGTLVQSGAVLMDPATGGIRALVGGRGEHVFRGFNRATQMKAQPGSTMKPLAVYTPALQSGYDVDSMLKDEKITYKGNYTPTNVGGVYSGEVPMYKAVANSINAPAVWLLDQIGIDKGVKSVEKFGITVPEKDRTLGLALGGMSKGASPVEMATAYATFANNGAKPESHIITKIVDPSGNTVYENVPKTKQIISETVSNEMTSMLLDVINTGTGQSAAVSGHEMAGKTGSTQVPFDDTSGTKDQWFVGYTPNLVGAVWMGYDKTDKEHYLTTTSSAGVSSLAHYVMNSGLQYQ 641
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633
   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  (0, 0)

(no "SCOP Domain" information available for 3ZG8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZG8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZG8)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8Y547_LISMO | Q8Y547)
molecular function
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8Y547_LISMO | Q8Y547: 3zg7 3zg9 3zga

(-) Related Entries Specified in the PDB File

3zg7 CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 4 FROM LISTERIA MONOCYTOGENES IN THE APO FORM
3zg9 CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 4 FROM LISTERIA MONOCYTOGENES IN THE CEFUROXIME BOUND FORM
3zga CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 4 FROM LISTERIA MONOCYTOGENES IN THE CARBENICILLIN BOUND FORM