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(-) Description

Title :  STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM AND THE ROLE OF STREPTOCOCCUS PNEUMONIAE PBP1B
 
Authors :  P. Macheboeuf, D. Lemaire, M. Jamin, O. Dideberg, A. Dessen
Date :  29 Apr 10  (Deposition) - 26 May 10  (Release) - 26 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Wall, Peptidoglycan Synthesis, Transferase, Multifunctional Enzyme, Pseudo-Substrate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Macheboeuf, D. Lemaire, M. Jamin, O. Dideberg, A. Dessen
Structural Insights Into The Catalytic Mechanism And The Role Of Streptococcus Pneumoniae Pbp1B
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 1B
    Chains: A, B
    EC Number: 2.3.2.-, 2.4.1.129
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4T1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 323-791
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: R6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2S2D2Ligand/IonN-BENZOYL-D-ALANINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:563 , GLN A:566 , LYS A:583 , HOH A:2054 , HOH A:2115 , HOH A:2116BINDING SITE FOR RESIDUE SO4 A1791
2AC2SOFTWAREALA A:459 , SER A:460 , SER A:516 , GLY A:653 , THR A:654BINDING SITE FOR RESIDUE S2D A1792
3AC3SOFTWARESER A:634 , SER B:634BINDING SITE FOR RESIDUE CL A1793
4AC4SOFTWAREARG A:627 , LYS A:633BINDING SITE FOR RESIDUE CL A1794
5AC5SOFTWARETHR B:563 , LYS B:583 , HOH B:2065 , HOH B:2132 , HOH B:2133 , HOH B:2134BINDING SITE FOR RESIDUE SO4 B1790
6AC6SOFTWAREALA B:459 , SER B:460 , SER B:516 , THR B:652 , GLY B:653 , THR B:654BINDING SITE FOR RESIDUE S2D B1791

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XD5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr B:371 -Gln B:372

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XD5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XD5)

(-) Exons   (0, 0)

(no "Exon" information available for 2XD5)

(-) 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:469
 aligned with Q7CRA4_STRR6 | Q7CRA4 from UniProtKB/TrEMBL  Length:821

    Alignment length:686
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784      
         Q7CRA4_STRR6   105 ISEITYSDGTVIASIESDLLRTSISSEQISENLKKAIIATEDEHFKEHKGVVPKAVIRATLGKFVGLGSSSGGSTLTQQLIKQQVVGDAPTLARKAAEIVDALALERAMNKDEILTTYLNVAPFGRNNKGQNIAGARQAAEGIFGVDASQLTVPQAAFLAGLPQSPITYSPYENTGELKSDEDLEIGLRRAKAVLYSMYRTGALSKDEYSQYKDYDLKQDFLPSGTVTGISRDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDDNHSLSRRAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSL 790
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....eeee.-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhh......eeeeeeee.....eeeee...................hhhhhhhhhhhhhhhhh.......eee.....................eeehhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhh..........hhhhh.....hhhhhhhhhhhhhh..ee.....eeeee.....eeee.....ee..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeeeee.hhh.eeeeeee...eeeeeeee.............hhhhhhhhhhhhhhhhhh...............eeeeee.......eeee....eeee...eeeeee.................hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xd5 A 105 ISEITYSDGTVIASI-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSL 790
                                   114    |    -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -  |    344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784      
                                        119                                                                                                                                                                                                                       337                                                                                                                                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:468
 aligned with Q7CRA4_STRR6 | Q7CRA4 from UniProtKB/TrEMBL  Length:821

    Alignment length:685
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784     
         Q7CRA4_STRR6   105 ISEITYSDGTVIASIESDLLRTSISSEQISENLKKAIIATEDEHFKEHKGVVPKAVIRATLGKFVGLGSSSGGSTLTQQLIKQQVVGDAPTLARKAAEIVDALALERAMNKDEILTTYLNVAPFGRNNKGQNIAGARQAAEGIFGVDASQLTVPQAAFLAGLPQSPITYSPYENTGELKSDEDLEIGLRRAKAVLYSMYRTGALSKDEYSQYKDYDLKQDFLPSGTVTGISRDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDDNHSLSRRAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGS 789
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------Transgly-2xd5---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Transpeptidase-2xd5B01 B:422-693                                                                                                                                                                                                                                                ------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -------Transgly-2xd5---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Transpeptidase-2xd5B02 B:422-693                                                                                                                                                                                                                                                ------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeee.....eeeee.....--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhh....-----.....hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhh......eeeeeeee.....eeeee...................hhhhhhhhhhhhhhhhh.......eee.....................eeehhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhh..........hhhhh.....hhhhhhhhhhhhhh..ee.....eeeeee....eeee.....ee..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeeeee......eeeeee...eeeeeeee.............hhhhhhhhhhhhhhhhhh...............eeeeee.......eeee....eeee...eeeeee.................hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xd5 B 105 ISEITYSDGTVIASIESDML--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DYLYFTTLAEAQERMYDYLAQRDNVSA-----EATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGS 789
                                   114       124         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -  |    344       354        |-    |  374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784     
                                             124                                                                                                                                                                                                                  337                       363   369
   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  (0, 0)

(no "SCOP Domain" information available for 2XD5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XD5)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Beta-lactamase (210)
(-)
Clan: no clan defined [family: Transgly] (8)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7CRA4_STRR6 | Q7CRA4)
molecular function
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
    GO:0008955    peptidoglycan glycosyltransferase activity    Catalysis of the reaction: [GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-diphosphoundecaprenol + GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = [GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-diphosphoundecaprenol + undecaprenyl diphosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
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
        Q7CRA4_STRR6 | Q7CRA4: 2uwx 2xd1 2y2g 2y2h 2y2i 2y2j 2y2k 2y2l 2y2m 2y2n 2y2o 2y2p 2y2q

(-) Related Entries Specified in the PDB File

2jch STRUCTURAL AND MECHANISTIC BASIS OF PENICILLIN BINDING PROTEIN INHIBITION BY LACTIVICINS
2uwx ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASS A PENICILLIN-BINDING PROTEINS
2xd1 ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASS A PENICILLIN-BINDING PROTEINS