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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TRANSPEPTIDASE DOMAIN OF NEISSERIA GONORRHOEAE PENICILLIN-BINDING PROTEIN 2 DERIVED FROM THE PENICILLIN-RESISTANT STRAIN 6140
 
Authors :  A. Fedarovich, C. Davies
Date :  22 Jul 14  (Deposition) - 03 Dec 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Penicillin-Binding Protein, Transpeptidase Domain, Peptidoglycan Synthesis, Antibiotic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Fedarovich, E. Cook, J. Tomberg, R. A. Nicholas, C. Davies
Structural Effect Of The Asp345A Insertion In Penicillin-Binding Protein 2 From Penicillin-Resistant Strains Of Neisseria Gonorrhoeae.
Biochemistry V. 53 7596 2014
PubMed-ID: 25403720  |  Reference-DOI: 10.1021/BI5011317

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 2
    Chains: A, B
    EC Number: 3.4.16.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-C2KV
    Expression System Strain: GW6011
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: TRANSPEPTIDASE DOMAIN (UNP RESIDUES 237-574)
    Gene: PENA
    Mutation: YES
    Organism Scientific: NEISSERIA GONORRHOEAE FA6140
    Organism Taxid: 528353
    Synonym: PBP-2

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4U3T)

(-) Sites  (0, 0)

(no "Site" information available for 4U3T)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U3T)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Asp A:346A-Thr A:347
2Val A:454 -Ala A:455
3Asn A:506 -Gly A:507
4Ala A:522 -Pro A:523
5Ala B:522 -Pro B:523

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U3T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U3T)

(-) Exons   (0, 0)

(no "Exon" information available for 4U3T)

(-) 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:322
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeee....hhhhhh...hhhhhhhhhhhhhhhh.......eee...eee..eee........eeehhhhhhh.hhhhhhhhhh..hhhhhhhhhhhh...................hhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhh.......hhhhh......eeeeeeeeeee.....eeeeeeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4u3t A  236 ALSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALANTPGRNRAVTDMIEPGSAIKPFVIAKALDAGKTDLNERLNTQPYKIGPSPVRDDTHVYPSLDVRGIMQKSSNVGTSKLSARFGAEEMYDFYHELGIGVRMHSGFPGETAGLLRNWRRWRPIEQATMSFGYGLQLSLLQLARAYTALTHDGVLLPLSFEKQAVAPQGKRIFKESTAREVRNLMVSVTEPGGTGTAGAVDGFDVGAKTGTARKLVNGRYVDNKHVGTFIGFAPAKNPRVIVAVTIDEPTAHGVVAGSPFKKIMGGSLNILGISPTKPLTA  574
                                   245       255       265       275      |299       309       319       329       339       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538  ||   552       562       572  
                                                                        282|                                              346A                                                                                                                                                                                                541|                            
                                                                         297                                                                                                                                                                                                                                                   546                            


Chain B from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeee....hhhhhh...hhhhhhhhhhhhhhhh.......eee...eee..eee........eeehhhhhhh.hhhhhhhhhh..hhhhhhhhhhhh...................hhhhh..hhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhh.......hhhhh......eeeeeeee...eeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4u3t B  236 ALSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALANTPGRNRAVTDMIEPGSAIKPFVIAKALDAGKTDLNERLNTQPYKIGPSPVRDDTHVYPSLDVRGIMQKSSNVGTSKLSARFGAEEMYDFYHELGIGVRMHSGFPGETAGLLRNWRRWRPIEQATMSFGYGLQLSLLQLARAYTALTHDGVLLPLSFEKQAVAPQGKRIFKESTAREVRNLMVSVTEPGGTGTAGAVDGFDVGAKTGTARKNKHVGTFIGFAPAKNPRVIVAVTIDEPTAHGGVVAGSPFKKIMGGSLNILGISPTKPLT  573
                                   245       255       265       275      |299       309       319       329       339       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498    || 516       526       536     ||549       559       569    
                                                                        282|                                              346A                                                                                                                                                          503|                           542|                           
                                                                         297                                                                                                                                                                                                             512                            546
   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 4U3T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U3T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U3T)

(-) Gene Ontology  (12, 12)

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  Cis Peptide Bonds
    Ala A:522 - Pro A:523   [ RasMol ]  
    Ala B:522 - Pro B:523   [ RasMol ]  
    Asn A:506 - Gly A:507   [ RasMol ]  
    Asp A:346A - Thr A:347   [ RasMol ]  
    Val A:454 - Ala A:455   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        PBP2_NEIGO | P08149: 3equ 3eqv 5ksh

(-) Related Entries Specified in the PDB File

3equ CRYSTAL STRUCTURE OF WILD-TYPE PENICILLIN-BINDING PROTEIN 2 FROM NEISSERIA GONORRHOEAE
3eqv CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 2 FROM NEISSERIA GONORRHOEAE CONTAINING FOUR MUTATIONS ASSOCIATED WITH PENICILLIN RESISTANCE