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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF AMPC BETA-LACTAMASE (AMPC(D)) FROM AN ESCHERICHIA COLI WITH A TRIPEPTIDE DELETION (GLY286 SER287 ASP288) ON THE H10 HELIX
 
Authors :  Y. Yamaguchi, G. Sato, Y. Yamagata, J. Wachino, Y. Arakawa, H. Kurosaki
Date :  29 Feb 08  (Deposition) - 10 Mar 09  (Release) - 16 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lactamase, Tripeptide Deletion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yamaguchi, G. Sato, Y. Yamagata, Y. Doi, J. Wachino, Y. Arakawa, K. Matsuda, H. Kurosaki
Structure Of Ampc Beta-Lactamase (Ampcd) From An Escherichia Coli Clinical Isolate With A Tripeptide Deletion (Gly286-Ser287-Asp288) In The H10 Helix
Acta Crystallogr. , Sect. F V. 65 540 2009
PubMed-ID: 19478427  |  Reference-DOI: 10.1107/S1744309109014249
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMPC
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBCKS+
    Expression System Strain: CS14-2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: HKY28
    Synonym: AMPC-EC5, AMPC-EC30, CLASS C BETA-LACTAMASE AMPC(D)

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1IPA2Ligand/IonISOPROPYL ALCOHOL
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL
2NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:100 , GLN A:136 , ASN A:137 , TRP A:138 , GLN A:139 , HOH A:468BINDING SITE FOR RESIDUE NA A 1
2AC2SOFTWAREARG A:148 , MET A:265 , TYR A:266 , GLU A:272 , HOH A:556BINDING SITE FOR RESIDUE IPA A 362
3AC3SOFTWAREHOH A:443 , GLN B:100 , GLN B:136 , ASN B:137 , TRP B:138 , GLN B:139BINDING SITE FOR RESIDUE NA B 2
4AC4SOFTWAREARG B:148 , MET B:265 , TYR B:266 , GLU B:272 , HOH B:510BINDING SITE FOR RESIDUE IPA B 362

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZJ9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:276 -Pro A:277
2Thr A:302 -Pro A:303
3Trp B:276 -Pro B:277
4Thr B:302 -Pro B:303

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZJ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZJ9)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZJ9)

(-) 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:355
 aligned with Q5EET9_ECOLX | Q5EET9 from UniProtKB/TrEMBL  Length:377

    Alignment length:358
                                    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       279       289       299       309       319       329       339       349       359       369        
         Q5EET9_ECOLX    20 APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMKTRVFQPLKLNHTWINVPSAEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDIIINGSDNKIALAARPVKPITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVAAAWQILNALQ 377
               SCOP domains d2zj9a_ A: automated matches                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2zj9A00 A:4-361 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhhh.hhhhhhhhhh........ee...hhhhhhhh..eee..eee......hhhhhhh.eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhh---.......ee.eeeeeee.....eeeeeeee....eeeeeeehhhheeeeeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zj9 A   4 APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMKTRVFQPLKLNHTWINVPSAEEKNYAWGYREGKAVHVSPRALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDIIIN---NKIALAARPVKPITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVAAAWQILNALQ 361
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283 |   | 293       303       313       323       333       343       353        
                                                                                                                                                                                                                                                                                                                   285 289                                                                        


Chain A from PDB  Type:PROTEIN  Length:355
 aligned with Q76DI4_ECOLX | Q76DI4 from UniProtKB/TrEMBL  Length:374

    Alignment length:355
                                    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       279       289       299       309       319       329       339       349       359       369     
         Q76DI4_ECOLX    20 APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMKTRVFQPLKLNHTWINVPSAEEKNYAWGYREGKAVHVSPRALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDIIINNKIALAARPVKPITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVAAAWQILNALQ 374
               SCOP domains d2zj9a_ A: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2zj9A00 A:4-361 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhhh.hhhhhhhhhh........ee...hhhhhhhh..eee..eee......hhhhhhh.eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhh.......ee.eeeeeee.....eeeeeeee....eeeeeeehhhheeeeeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zj9 A   4 APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMKTRVFQPLKLNHTWINVPSAEEKNYAWGYREGKAVHVSPRALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDIIINNKIALAARPVKPITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVAAAWQILNALQ 361
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283 ||    296       306       316       326       336       346       356     
                                                                                                                                                                                                                                                                                                                   285|                                                                        
                                                                                                                                                                                                                                                                                                                    289                                                                        


Chain B from PDB  Type:PROTEIN  Length:355
 aligned with Q5EET9_ECOLX | Q5EET9 from UniProtKB/TrEMBL  Length:377

    Alignment length:358
                                    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       279       289       299       309       319       329       339       349       359       369        
         Q5EET9_ECOLX    20 APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMKTRVFQPLKLNHTWINVPSAEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDIIINGSDNKIALAARPVKPITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVAAAWQILNALQ 377
               SCOP domains d2zj9b_ B: automated matches                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2zj9B00 B:4-361 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) --------Beta-lactamase-2zj9B01 B:12-361                                                                                                                                                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) --------Beta-lactamase-2zj9B02 B:12-361                                                                                                                                                                                                                                                                                                                                Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhhh.hhhhhhhhhh........ee...hhhhhhhh..eee..eee......hhhhhhh.eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhh---.......ee.eeeeeee.....eeeeeeee....eeeeeeehhhheeeeeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zj9 B   4 APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMKTRVFQPLKLNHTWINVPSAEEKNYAWGYREGKAVHVSPRALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDIIIN---NKIALAARPVKPITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVAAAWQILNALQ 361
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283 |   | 293       303       313       323       333       343       353        
                                                                                                                                                                                                                                                                                                                   285 289                                                                        


Chain B from PDB  Type:PROTEIN  Length:355
 aligned with Q76DI4_ECOLX | Q76DI4 from UniProtKB/TrEMBL  Length:374

    Alignment length:355
                                    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       279       289       299       309       319       329       339       349       359       369     
         Q76DI4_ECOLX    20 APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMKTRVFQPLKLNHTWINVPSAEEKNYAWGYREGKAVHVSPRALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDIIINNKIALAARPVKPITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVAAAWQILNALQ 374
               SCOP domains d2zj9b_ B: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2zj9B00 B:4-361 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) --------Beta-lactamase-2zj9B01 B:12-361                                                                                                                                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) --------Beta-lactamase-2zj9B02 B:12-361                                                                                                                                                                                                                                                                                                                             Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhhh.hhhhhhhhhh........ee...hhhhhhhh..eee..eee......hhhhhhh.eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhh.......ee.eeeeeee.....eeeeeeee....eeeeeeehhhheeeeeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zj9 B   4 APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMKTRVFQPLKLNHTWINVPSAEEKNYAWGYREGKAVHVSPRALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDIIINNKIALAARPVKPITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVAAAWQILNALQ 361
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283 ||    296       306       316       326       336       346       356     
                                                                                                                                                                                                                                                                                                                   285|                                                                        
                                                                                                                                                                                                                                                                                                                    289
   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  (1, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (5, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5EET9_ECOLX | Q5EET9)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

Chain A,B   (Q76DI4_ECOLX | Q76DI4)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

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  2zj9
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 Related Entries

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