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(-) Description

Title :  STRUCTURE OF PBP-A ACYL-ENZYME COMPLEX WITH PENICILLIN-G
 
Authors :  C. Evrard, J. P. Declercq
Date :  31 Oct 06  (Deposition) - 27 Nov 07  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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
    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  (1, 4)

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

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
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:2182BINDING SITE FOR RESIDUE PNM A1275
2AC2SOFTWAREALA B:60 , SER B:61 , GLU B:96 , ALA B:97 , SER B:122 , ASN B:124 , MET B:161 , THR B:202 , LYS B:219 , THR B:220 , GLY B:221 , ASP B:222 , HOH B:2207 , HOH B:2208BINDING SITE FOR RESIDUE PNM B1275
3AC3SOFTWAREALA C:60 , SER C:61 , GLU C:96 , ALA C:97 , SER C:122 , ASN C:124 , MET C:161 , THR C:202 , LYS C:219 , THR C:220 , GLY C:221 , ASP C:222 , HOH C:2205 , HOH C:2217BINDING SITE FOR RESIDUE PNM C1275
4AC4SOFTWAREARG C:30 , ALA D:60 , SER D:61 , GLU D:96 , ALA D:97 , SER D:122 , ASN D:124 , PRO D:159 , MET D:161 , LYS D:219 , THR D:220 , GLY D:221 , ASP D:222 , ILE D:223 , GLY D:224 , HOH D:2196 , HOH D:2205BINDING SITE FOR RESIDUE PNM D1275

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J8Y)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J8Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J8Y)

(-) Exons   (0, 0)

(no "Exon" information available for 2J8Y)

(-) 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: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....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
                 2j8y A  10 TLPPERPLTNLQQQIQQLVSRQPNLTAGLYFFNLDSGASLNVGGDQVFPAASTIKFPILVAFFKAVDEGRVTLQERLTMRPDLIAPEAGTLQYQKPNSQYAALEVAELMITISDNTATNMIIDRLGGAAELNQQFQEWGLENTVINNPLPDMKGTNTTSPRDLATLMLKIGQGEILSPRSRDRLLDIMRRTVTNTLLPAGLGKGATIAHKTGDIGIVVGDAGMVDMPNGQRYVAAMMVKRPYNDPRGSELIRQVSRMVYQAFEKL 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 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....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
                 2j8y B  10 TLPPERPLTNLQQQIQQLVSRQPNLTAGLYFFNLDSGASLNVGGDQVFPAASTIKFPILVAFFKAVDEGRVTLQERLTMRPDLIAPEAGTLQYQKPNSQYAALEVAELMITISDNTATNMIIDRLGGAAELNQQFQEWGLENTVINNPLPDMKGTNTTSPRDLATLMLKIGQGEILSPRSRDRLLDIMRRTVTNTLLPAGLGKGATIAHKTGDIGIVVGDAGMVDMPNGQRYVAAMMVKRPYNDPRGSELIRQVSRMVYQAFEKL 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
                 2j8y C  11 LPPERPLTNLQQQIQQLVSRQPNLTAGLYFFNLDSGASLNVGGDQVFPAASTIKFPILVAFFKAVDEGRVTLQERLTMRPDLIAPEAGTLQYQKPNSQYAALEVAELMITISDNTATNMIIDRLGGAAELNQQFQEWGLENTVINNPLPDMKGTNTTSPRDLATLMLKIGQGEILSPRSRDRLLDIMRRTVTNTLLPAGLGKGATIAHKTGDIGIVVGDAGMVDMPNGQRYVAAMMVKRPYNDPRGSELIRQVSRMVYQAFEKL 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:273
 aligned with Q8DH45_THEEB | Q8DH45 from UniProtKB/TrEMBL  Length:368

    Alignment length:273
                                   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 PAPEAPTSTLPPERPLTNLQQQIQQLVSRQPNLTAGLYFFNLDSGASLNVGGDQVFPAASTIKFPILVAFFKAVDEGRVTLQERLTMRPDLIAPEAGTLQYQKPNSQYAALEVAELMITISDNTATNMIIDRLGGAAELNQQFQEWGLENTVINNPLPDMKGTNTTSPRDLATLMLKIGQGEILSPRSRDRLLDIMRRTVTNTLLPAGLGKGATIAHKTGDIGIVVGDAGMVDMPNGQRYVAAMMVKRPYNDPRGSELIRQVSRMVYQAFEKL 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....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j8y D   2 PAPEAPTSTLPPERPLTNLQQQIQQLVSRQPNLTAGLYFFNLDSGASLNVGGDQVFPAASTIKFPILVAFFKAVDEGRVTLQERLTMRPDLIAPEAGTLQYQKPNSQYAALEVAELMITISDNTATNMIIDRLGGAAELNQQFQEWGLENTVINNPLPDMKGTNTTSPRDLATLMLKIGQGEILSPRSRDRLLDIMRRTVTNTLLPAGLGKGATIAHKTGDIGIVVGDAGMVDMPNGQRYVAAMMVKRPYNDPRGSELIRQVSRMVYQAFEKL 274
                                    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)
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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 2J8Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J8Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J8Y)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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  2j8y
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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