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(-) Description

Title :  CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 2 FROM NEISSERIA GONORRHOEAE CONTAINING AN A501T MUTATION ASSOCIATED WITH CEPHALOSPORIN RESISTANCE
 
Authors :  A. Fedarovich, C. Davies
Date :  08 Jul 16  (Deposition) - 01 Mar 17  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Biosynthetic Protein, Class B Transpeptidase, Peptidoglycan Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Tomberg, A. Fedarovich, L. R. Vincent, A. E. Jerse, M. Unemo, C. Davies, R. A. Nicholas
Alanine 501 Mutations In Penicillin-Binding Protein 2 From Neisseria Gonorrhoeae: Structure, Mechanism, And Effects On Cephalosporin Resistance And Biological Fitness.
Biochemistry V. 56 1140 2017
PubMed-ID: 28145684  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B01030

(-) 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/H6
    Expression System Strain: GW6011
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PENA
    Mutation: YES
    Organism Scientific: NEISSERIA GONORRHOEAE
    Organism Taxid: 485
    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  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SEP2Mod. Amino AcidPHOSPHOSERINE
3SO412Ligand/IonSULFATE ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SEP1Mod. Amino AcidPHOSPHOSERINE
3SO45Ligand/IonSULFATE ION
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SEP1Mod. Amino AcidPHOSPHOSERINE
3SO47Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:190 , GLY A:191 , ARG A:298 , ASN A:299 , PRO A:397binding site for residue GOL A 601
02AC2SOFTWAREARG A:67 , ARG A:211 , ARG B:408binding site for residue SO4 A 602
03AC3SOFTWAREARG A:288 , PRO A:289 , GLY A:290 , ARG A:291binding site for residue SO4 A 603
04AC4SOFTWARESER A:294 , ARG A:297binding site for residue SO4 A 604
05AC5SOFTWAREVAL A:390 , ARG A:391 , HIS A:393binding site for residue SO4 A 605
06AC6SOFTWAREARG A:81 , LYS A:451binding site for residue SO4 A 606
07AC7SOFTWAREGLU B:190 , GLY B:191 , ARG B:297 , ARG B:298 , ASN B:299 , THR B:303 , PRO B:397binding site for residue GOL B 601
08AC8SOFTWARETYR B:284 , ASP B:285 , ARG B:288 , ARG B:291 , ALA B:292 , GLN B:296 , SO4 B:608binding site for residue GOL B 602
09AC9SOFTWARESER B:342 , LYS B:361 , ARG B:411binding site for residue SO4 B 603
10AD1SOFTWAREGLN A:457 , ARG B:288binding site for residue SO4 B 604
11AD2SOFTWAREARG B:288 , PRO B:289 , GLY B:290binding site for residue SO4 B 605
12AD3SOFTWARESER B:294 , ARG B:297binding site for residue SO4 B 606
13AD4SOFTWAREGLU A:59 , GLN A:60 , ARG B:345 , ASN B:406 , ARG B:409binding site for residue SO4 B 607
14AD5SOFTWAREPRO A:446 , ARG B:291 , GOL B:602binding site for residue SO4 B 608
15AD6SOFTWAREASP B:293 , SER B:294 , ARG B:297binding site for residue SO4 B 609

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KSH)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr A:281 -Pro A:282
2Ala A:522 -Pro A:523
3Thr B:281 -Pro B:282
4Ala B:522 -Pro B:523

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KSH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KSH)

(-) Exons   (0, 0)

(no "Exon" information available for 5KSH)

(-) 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:450
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh......eeeeeee......ee.....eeeeee....eee..hhhhhhhhhh.........hhhhhhhhhhhhee.eeeeeee.....eeee.........ee...ee...hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhh........ee...eee..eee.......eehhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...................hhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhhhh.....hhhhh......eeeeeeeeeee..eeeeeeeeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ksh A  53 TYNFLKEQGDNRIVRTQALPATRGTVSDRNGAVLALSAPTELKRHYPMGNLFAHVIGFTDIDGKGQEGLELSLEDSLYGEDGAEVVLRDRQGNIVDSLDSPRNKAPQNGKDIILSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALANTPAYDPNRPGRADSEQRRNRAVTDMIEPGSAIKPFVIAKALDAGKTDLNERLNTQPYKIGPSPVRDTHVYPSLDVRGIMQKSSNVGTSKLSARFGAEEMYDFYHELGIGVRMHSGFPGETAGLLRNWRRWRPIEQATMSFGYGLQLSLLQLARAYTALTHDGVLLPLSFEKQAVAPQGKRIFKEsTAREVRNLMVSVTEPGGTGTAGAVDGFDVGAKTGTTRKLVNGRYVDNKHVGTFIGFAPAKNPRVIVAVTIDEPTAHGYYGGVVAGSPFKKIMGGSLNILGISPTKPLT 573
                                    62        72        82        92|      173       183       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
                                                                  92|                                                                                                                                                                                                                                                                                                          465-SEP                                                                                                        
                                                                  164                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:436
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......ee.....eeeeeee...eeee..hhhhhhhhhh.........hhhhhhhhhhhhh..eeeeee.....ee..............ee...hhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhh........ee...eee..eee.......eehhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...................hhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhh.......hhhhh......eeeeeeeeeee..eeeeeeeeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ksh B  65 IVRTQALPATRGTVSDRNGAVLALSAPTEELKRHYPMGNLFAHVIGFTDIDGKGQEGLELSLEDSLYGEDGAEVVLRDNIVDSLDSPRNKAPQNGKDIILSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALANTPAYDPNRPGRADSEQRRNRAVTDMIEPGSAIKPFVIAKALDAGKTDLNERLNTQPYKIGPSPVRDTHVYPSLDVRGIMQKSSNVGTSKLSARFGAEEMYDFYHELGIGVRMHSGFPGETAGLLRNWRRWRPIEQATMSFGYGLQLSLLQLARAYTALTHDGVLLPLSFEKQAVAPQGKRIFKEsTAREVRNLMVSVTEPGGTGTAGAVDGFDVGAKTGTTRKLVNGRYVDNKHVGTFIGFAPAKNPRVIVAVTIDEPTAHGYYGGVVAGSPFKKIMGGSLNILGISPTKPLT 573
                                    74        84       164       174       184       194       204       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567      
                                                       93|                                             212|                                                                                                                                                                                                                                                      465-SEP                                                                                                        
                                                       164                                              216
   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 5KSH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KSH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KSH)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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        PBP2_NEIGO | P08149: 3equ 3eqv 4u3t

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