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(-) Description

Title :  STRUCTURE OF PBP-A, L158E MUTANT. ACYL-ENZYME COMPLEX WITH PENICILLIN-G.
 
Authors :  C. Evrard, J. -P. Declercq
Date :  06 Dec 06  (Deposition) - 05 Feb 08  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Penicillin-Binding Protein, Hydrolase, Lactamase, Thioesterase, Dd-Peptidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Urbach, C. Evrard, V. Pudzaitis, J. Fastrez, P. Soumillion, J. -P. Declercq
Structure Of Pbp-A From Thermosynechococcus Elongatus, A Penicillin-Binding Protein Closely Related To Class A Beta-Lactamases.
J. Mol. Biol. V. 386 109 2009
PubMed-ID: 19100272  |  Reference-DOI: 10.1016/J.JMB.2008.12.001

(-) Compounds

Molecule 1 - TLL2115 PROTEIN
    Chains: A, B, C, D
    EC Number: 3.4.16.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD-MYC-HIS-TETR
    Expression System Strain: TOP 10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 93-368
    Mutation: YES
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
    Organism Taxid: 32046
    Other Details: CYANOBASE
    Strain: BP-1
    Synonym: SERINE-TYPE CARBOXYPEPTIDASE FROM THERMOSYNECHOCOCCUS ELONGATUS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PNM4Ligand/IonOPEN FORM - PENICILLIN G
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PNM1Ligand/IonOPEN FORM - PENICILLIN G
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PNM1Ligand/IonOPEN FORM - PENICILLIN G
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PNM1Ligand/IonOPEN FORM - PENICILLIN G
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PNM1Ligand/IonOPEN FORM - PENICILLIN G

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:60 , SER A:61 , GLU A:96 , ALA A:97 , SER A:122 , ASN A:124 , MET A:161 , THR A:202 , LYS A:219 , THR A:220 , GLY A:221 , ASP A:222 , HOH A:2088 , HOH A:2121 , HOH A:2157BINDING SITE FOR RESIDUE PNM A 300
2AC2SOFTWAREALA B:60 , SER B:61 , GLU B:96 , ALA B:97 , SER B:122 , ASN B:124 , PRO B:159 , MET B:161 , LYS B:219 , THR B:220 , GLY B:221 , ASP B:222 , HOH B:2151 , HOH B:2185 , HOH B:2202 , HOH B:2226BINDING SITE FOR RESIDUE PNM B 300
3AC3SOFTWAREALA C:60 , SER C:61 , GLU C:96 , SER C:122 , ASN C:124 , MET C:161 , THR C:202 , LYS C:219 , THR C:220 , ASP C:222 , HOH C:2227 , HOH C:2260BINDING SITE FOR RESIDUE PNM C 300
4AC4SOFTWAREGLN C:26 , ARG C:30 , ALA D:60 , SER D:61 , GLU D:96 , ALA D:97 , SER D:122 , PRO D:159 , MET D:161 , LYS D:219 , THR D:220 , GLY D:221 , ASP D:222BINDING SITE FOR RESIDUE PNM D 300
5AC5SOFTWAREGLN A:181 , HOH A:2129 , ASP D:76 , SER D:186 , HOH D:2061BINDING SITE FOR RESIDUE GOL A2647

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:158 -Pro A:159
2Glu B:158 -Pro B:159
3Glu C:158 -Pro C:159
4Glu D:158 -Pro D:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2JBF)

(-) 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:264
 aligned with Q8DH45_THEEB | Q8DH45 from UniProtKB/TrEMBL  Length:368

    Alignment length:264
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    
         Q8DH45_THEEB   102 LPPERPLTNLQQQIQQLVSRQPNLTAGLYFFNLDSGASLNVGGDQVFPAASTIKFPILVAFFKAVDEGRVTLQERLTMRPDLIAPEAGTLQYQKPNSQYAALEVAELMITISDNTATNMIIDRLGGAAELNQQFQEWGLENTVINNPLPDMKGTNTTSPRDLATLMLKIGQGEILSPRSRDRLLDIMRRTVTNTLLPAGLGKGATIAHKTGDIGIVVGDAGMVDMPNGQRYVAAMMVKRPYNDPRGSELIRQVSRMVYQAFEKL 365
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eehhhhhhhhhhhhhh....eeeeeeee....eeeee.....ee.hhhhhhhhhhhhhhhhhh.......eee.hhhhh.....hhhhh....eeehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh..................eehhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhh....eeeeeeee...eeeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2jbf A  11 LPPERPLTNLQQQIQQLVSRQPNLTAGLYFFNLDSGASLNVGGDQVFPAASTIKFPILVAFFKAVDEGRVTLQERLTMRPDLIAPEAGTLQYQKPNSQYAALEVAELMITISDNTATNMIIDRLGGAAELNQQFQEWGLENTVINNPEPDMKGTNTTSPRDLATLMLKIGQGEILSPRSRDRLLDIMRRTVTNTLLPAGLGKGATIAHKTGDIGIVVGDAGMVDMPNGQRYVAAMMVKRPYNDPRGSELIRQVSRMVYQAFEKL 274
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    


Chain B from PDB  Type:PROTEIN  Length:265
 aligned with Q8DH45_THEEB | Q8DH45 from UniProtKB/TrEMBL  Length:368

    Alignment length:265
                                   110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360     
         Q8DH45_THEEB   101 TLPPERPLTNLQQQIQQLVSRQPNLTAGLYFFNLDSGASLNVGGDQVFPAASTIKFPILVAFFKAVDEGRVTLQERLTMRPDLIAPEAGTLQYQKPNSQYAALEVAELMITISDNTATNMIIDRLGGAAELNQQFQEWGLENTVINNPLPDMKGTNTTSPRDLATLMLKIGQGEILSPRSRDRLLDIMRRTVTNTLLPAGLGKGATIAHKTGDIGIVVGDAGMVDMPNGQRYVAAMMVKRPYNDPRGSELIRQVSRMVYQAFEKL 365
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhhhhhhhhhhh....eeeeeeee....eeee......ee.hhhhhhhhhhhhhhhhhh.......eee.hhhhh.....hhhhh....eeehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh..................eehhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhh....eeeeeeee...eeeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jbf B  10 TLPPERPLTNLQQQIQQLVSRQPNLTAGLYFFNLDSGASLNVGGDQVFPAASTIKFPILVAFFKAVDEGRVTLQERLTMRPDLIAPEAGTLQYQKPNSQYAALEVAELMITISDNTATNMIIDRLGGAAELNQQFQEWGLENTVINNPEPDMKGTNTTSPRDLATLMLKIGQGEILSPRSRDRLLDIMRRTVTNTLLPAGLGKGATIAHKTGDIGIVVGDAGMVDMPNGQRYVAAMMVKRPYNDPRGSELIRQVSRMVYQAFEKL 274
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269     


Chain C from PDB  Type:PROTEIN  Length:264
 aligned with Q8DH45_THEEB | Q8DH45 from UniProtKB/TrEMBL  Length:368

    Alignment length:264
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    
         Q8DH45_THEEB   102 LPPERPLTNLQQQIQQLVSRQPNLTAGLYFFNLDSGASLNVGGDQVFPAASTIKFPILVAFFKAVDEGRVTLQERLTMRPDLIAPEAGTLQYQKPNSQYAALEVAELMITISDNTATNMIIDRLGGAAELNQQFQEWGLENTVINNPLPDMKGTNTTSPRDLATLMLKIGQGEILSPRSRDRLLDIMRRTVTNTLLPAGLGKGATIAHKTGDIGIVVGDAGMVDMPNGQRYVAAMMVKRPYNDPRGSELIRQVSRMVYQAFEKL 365
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eehhhhhhhhhhhhhh....eeeeeeee....eeee......ee.hhhhhhhhhhhhhhhhhh.......eee...........hhhhh....eeehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh..................eehhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhh....eeeeeeee...eeeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2jbf C  11 LPPERPLTNLQQQIQQLVSRQPNLTAGLYFFNLDSGASLNVGGDQVFPAASTIKFPILVAFFKAVDEGRVTLQERLTMRPDLIAPEAGTLQYQKPNSQYAALEVAELMITISDNTATNMIIDRLGGAAELNQQFQEWGLENTVINNPEPDMKGTNTTSPRDLATLMLKIGQGEILSPRSRDRLLDIMRRTVTNTLLPAGLGKGATIAHKTGDIGIVVGDAGMVDMPNGQRYVAAMMVKRPYNDPRGSELIRQVSRMVYQAFEKL 274
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    


Chain D from PDB  Type:PROTEIN  Length:274
 aligned with Q8DH45_THEEB | Q8DH45 from UniProtKB/TrEMBL  Length:368

    Alignment length:274
                                   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    
         Q8DH45_THEEB    93 PAPEAPTSTLPPERPLTNLQQQIQQLVSRQPNLTAGLYFFNLDSGASLNVGGDQVFPAASTIKFPILVAFFKAVDEGRVTLQERLTMRPDLIAPEAGTLQYQKPNSQYAALEVAELMITISDNTATNMIIDRLGGAAELNQQFQEWGLENTVINNPLPDMKGTNTTSPRDLATLMLKIGQGEILSPRSRDRLLDIMRRTVTNTLLPAGLGKGATIAHKTGDIGIVVGDAGMVDMPNGQRYVAAMMVKRPYNDPRGSELIRQVSRMVYQAFEKLS 366
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------Beta-lactamase2-2jbfD01 D:43-245                                                                                                                                                                           ------------------------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------Beta-lactamase2-2jbfD02 D:43-245                                                                                                                                                                           ------------------------------ Pfam domains (2)
           Pfam domains (3) -----------------------------------------Beta-lactamase2-2jbfD03 D:43-245                                                                                                                                                                           ------------------------------ Pfam domains (3)
           Pfam domains (4) -----------------------------------------Beta-lactamase2-2jbfD04 D:43-245                                                                                                                                                                           ------------------------------ Pfam domains (4)
         Sec.struct. author .............eehhhhhhhhhhhhhh....eeeeeeee....eeee......ee.hhhhhhhhhhhhhhhhhh.......eee.hhhhh.....hhhhh....eeehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh..................eehhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhh....eeeeeeee...eeeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jbf D   2 PAPEAPTSTLPPERPLTNLQQQIQQLVSRQPNLTAGLYFFNLDSGASLNVGGDQVFPAASTIKFPILVAFFKAVDEGRVTLQERLTMRPDLIAPEAGTLQYQKPNSQYAALEVAELMITISDNTATNMIIDRLGGAAELNQQFQEWGLENTVINNPEPDMKGTNTTSPRDLATLMLKIGQGEILSPRSRDRLLDIMRRTVTNTLLPAGLGKGATIAHKTGDIGIVVGDAGMVDMPNGQRYVAAMMVKRPYNDPRGSELIRQVSRMVYQAFEKLS 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
   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 2JBF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Beta-lactamase (210)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2JBF)

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  2jbf
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 Related Entries

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

UniProtKB/TrEMBL
        Q8DH45_THEEB | Q8DH45: 2j7v 2j8y 2j9o

(-) Related Entries Specified in the PDB File

2j7v STRUCTURE OF PBP-A
2j8y STRUCTURE OF PBP-A ACYL-ENZYME COMPLEX WITH PENICILLIN-G
2j9o STRUCTURE OF PBP-A, L158E MUTANT