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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI PENICILLIN-BINDING PROTEIN 5 IN COMPLEX WITH A PEPTIDE-MIMETIC CEPHALOSPORIN
 
Authors :  A. J. Powell, C. Davies
Date :  16 Nov 07  (Deposition) - 26 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Peptidoglycan Synthesis, Penicillin-Binding Protein, Dd- Carboxypeptidase, Hydrolase, Designed Cephalosporin, Cell Shape, Cell Wall Biogenesis/Degradation, Inner Membrane, Membrane, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Sauvage, A. J. Powell, J. Heilemann, H. R. Josephine, P. Charlier, C. Davies, R. F. Pratt
Crystal Structures Of Complexes Of Bacterial Dd-Peptidases With Peptidoglycan-Mimetic Ligands: The Substrate Specificity Puzzle
J. Mol. Biol. V. 381 383 2008
PubMed-ID: 18602645  |  Reference-DOI: 10.1016/J.JMB.2008.06.012

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 5
    ChainsA
    EC Number3.4.16.4, 3.5.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBR322
    Expression System StrainMC1061
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABASE RESIDUES 30-386
    GeneDACA, PFV
    Organism ScientificESCHERICHIA COLI
    SynonymDD- PEPTIDASE, DD-CARBOXYPEPTIDASE, BETA-LACTAMASE, D- ALANYL-D-ALANINE CARBOXYPEPTIDASE DACA, PBP-5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2HJ21Ligand/Ion(2R)-2-[(R)-{[(6S)-6-AMINO-6-CARBOXYHEXANOYL]AMINO}(CARBOXY)METHYL]-5-METHYL-3,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:52 , TYR A:136 , ALA A:139 , LEU A:140 , ASP A:175BINDING SITE FOR RESIDUE GOL A 364
2AC2SOFTWAREALA A:43 , SER A:44 , ARG A:198 , THR A:214 , GLY A:215 , HIS A:216 , PHE A:245 , ARG A:248BINDING SITE FOR RESIDUE HJ2 A 500
3AC3SOFTWAREASN A:107 , LEU A:108 , TYR A:183 , ASN A:197 , ASN A:199 , ILE A:212 , LYS A:213 , THR A:214 , HOH A:528 , HOH A:574BINDING SITE FOR RESIDUE GOL A 365
4AC4SOFTWAREASP A:74 , ASN A:80 , VAL A:116 , GLN A:126 , HIS A:151BINDING SITE FOR RESIDUE GOL A 366
5AC5SOFTWARETYR A:25 , ASN A:26 , GLN A:170 , ARG A:174 , TYR A:297 , HOH A:597 , HOH A:672BINDING SITE FOR RESIDUE GOL A 367

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:211 -Ile A:212
2Ala A:321 -Pro A:322

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_DACA_ECOLI_001 *G134DDACA_ECOLI  ---  ---AG105D
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BEC)

(-) 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:352
 aligned with DACA_ECOLI | P0AEB2 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:352
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382  
           DACA_ECOLI    33 NIKTMIPGVPQIDAESYILIDYNSGKVLAEQNADVRRDPASLTKMMTSYVIGQAMKAGKFKETDLVTIGNDAWATGNPVFKGSSLMFLKPGMQVPVSQLIRGINLQSGNDACVAMADFAAGSQDAFVGLMNSYVNALGLKNTHFQTVHGLDADGQYSSARDMALIGQALIRDVPNEYSIYKEKEFTFNGIRQLNRNGLLWDNSLNVDGIKTGHTDKAGYNLVASATEGQMRLISAVMGGRTFKGREAESKKLLTWGFRFFETVNPLKVGKEFASEPVWFGDSDRASLGVDKDVYLTIPRGRMKDLKASYVLNSSELHAPLQKNQVVGTINFQLDGKTIEQRPLVVLQEIPEG 384
               SCOP domains d3beca2 A:4-262 Penicillin-binding protein 5, N-terminal domain                                                                                                                                                                                                    d3beca1 A:263-355 Penicillin-binding protein 5, C-terminal domain                             SCOP domains
               CATH domains 3becA01 A:4-262 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                            3becA02 A:263-354 Peptidoglycan synthesis regulatory factor (PBP3), Domain 2                - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeee.....eeeee.......hhhhhhhhhhhhhhhhhhh.......eee.hhhhhhhhhhhhh...........eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee..hhhhhh....eeeeeeeee...eeeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhheeeeeee......eeeeee.....eeeee....eeeeee.hhhhhheeeeee....ee.......eeeeeeeee..eeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------D---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bec A   4 NIKTMIPGVPQIDAESYILIDYNSGKVLAEQNADVRRDPASLTKMMTSYVIGQAMKAGKFKETDLVTIGNDAWATGNPVFKGSSLMFLKPGMQVPVSQLIRGINLQSGNDACVAMADFAAGSQDAFVGLMNSYVNALGLKNTHFQTVHGLDADGQYSSARDMALIGQALIRDVPNEYSIYKEKEFTFNGIRQLNRNGLLWDNSLNVDGIKTGHTDKAGYNLVASATEGQMRLISAVMGGRTFKGREAESKKLLTWGFRFFETVNPLKVGKEFASEPVWFGDSDRASLGVDKDVYLTIPRGRMKDLKASYVLNSSELHAPLQKNQVVGTINFQLDGKTIEQRPLVVLQEIPEG 355
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353  

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DACA_ECOLI | P0AEB2)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0009002    serine-type D-Ala-D-Ala carboxypeptidase activity    Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
biological process
    GO:0044036    cell wall macromolecule metabolic process    The chemical reactions and pathways involving macromolecules forming, or destined to form, part of the cell wall. A cell wall is a rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0000270    peptidoglycan metabolic process    The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only in bacterial cell walls and consisting of strands of glycosaminoglycan cross-linked by oligopeptides to form a huge and rigid network.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005887    integral component of plasma membrane    The component of the plasma 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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DACA_ECOLI | P0AEB21hd8 1nj4 1nzo 1nzu 1sdn 1z6f 3beb 3mzd 3mze 3mzf 5j8x

(-) Related Entries Specified in the PDB File

3beb