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(-) Description

Title :  STRUCTURAL BASIS FOR THE EXTENDED SUBSTRATE SPECTRUM OF CMY-10, A PLASMID-ENCODED CLASS C BETA-LACTAMASE
 
Authors :  S. S. Cha, H. I. Jung, Y. J. An, S. H. Lee
Date :  03 May 05  (Deposition) - 18 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Extended Spectrum Beta-Lactamase, Cmy-10, Plasmid, Class C, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Y. Kim, H. I. Jung, Y. J. An, J. H. Lee, S. J. Kim, S. H. Jeong, K. J. Lee, P. G. Suh, H. S. Lee, S. H. Lee, S. S. Cha
Structural Basis For The Extended Substrate Spectrum Of Cmy-10, A Plasmid-Encoded Class C Beta-Lactamase.
Mol. Microbiol. V. 60 907 2006
PubMed-ID: 16677302  |  Reference-DOI: 10.1111/J.1365-2958.2006.05146.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EXTENDED-SPECTRUM BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ENTEROBACTER AEROGENES
    Organism Taxid: 548
    Synonym: CMY-10

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2ZN8Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:7 , HIS A:40BINDING SITE FOR RESIDUE ZN A 506
02AC2SOFTWAREHIS A:148 , HOH A:1566 , HOH A:1571 , HOH A:1699BINDING SITE FOR RESIDUE ZN A 507
03AC3SOFTWAREHIS A:161 , ACY A:1403 , ACY A:1404BINDING SITE FOR RESIDUE ZN A 508
04AC4SOFTWAREHIS A:187 , HOH A:1493 , HOH A:1641BINDING SITE FOR RESIDUE ZN A 509
05AC5SOFTWAREASN A:191 , HOH A:1444 , HOH A:1446 , HOH A:1474 , HOH A:1476 , HOH A:1595BINDING SITE FOR RESIDUE ZN A 510
06AC6SOFTWAREGLY A:359BINDING SITE FOR RESIDUE ZN A 511
07AC7SOFTWAREHIS A:24 , TYR A:341 , ACY A:1401BINDING SITE FOR RESIDUE ZN A 512
08AC8SOFTWAREASP A:14 , HOH A:1640 , HOH A:1683 , HOH A:1684BINDING SITE FOR RESIDUE ZN A 514
09AC9SOFTWAREGLU A:23 , HIS A:24 , ZN A:512 , HOH A:1551BINDING SITE FOR RESIDUE ACY A 1401
10BC1SOFTWAREVAL A:213 , ASN A:214 , THR A:316 , ASN A:317 , HOH A:1470BINDING SITE FOR RESIDUE ACY A 1402
11BC2SOFTWAREHIS A:93 , TRP A:96 , HIS A:161 , SER A:165 , ZN A:508 , ACY A:1404 , HOH A:1455BINDING SITE FOR RESIDUE ACY A 1403
12BC3SOFTWARESER A:129 , MET A:132 , ARG A:133 , HIS A:161 , ZN A:508 , ACY A:1403BINDING SITE FOR RESIDUE ACY A 1404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZKJ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:276 -Pro A:277

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZKJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZKJ)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZKJ)

(-) Sequences/Alignments

Asymmetric/Biological 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:350
 aligned with Q99QC1_ENTAE | Q99QC1 from UniProtKB/TrEMBL  Length:382

    Alignment length:353
                                    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       379   
         Q99QC1_ENTAE    30 DPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGAGVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAPLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLRFVKANIGGVDDKALQQAISLTHQGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIEARIKAAHAILAQLAG 382
               SCOP domains d1zkja_ A: automated matches                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1zkjA00 A:7-359 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------Beta-lactamase-1zkjA01 A:13-358                                                                                                                                                                                                                                                                                                                           - Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...............ee...hhhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhh.hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhh..ee.....ee......hhhhhhh.eehhhhhhhhhhhh.....hhhhhhhhhhh....eee..eee....eeee...hhhhhhhhhhhhhhhh.ee......---.eeeeeeeee..eeeeeeeehhhheeeeeee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zkj A   7 DPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGAGVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAPLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLRFVKANIGGVDDKALQQAISLTHQGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRE---QVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIEARIKAAHAILAQLAG 359
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296      |  -|      316       326       336       346       356   
                                                                                                                                                                                                                                                                                                                                  303 307
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q99QC1_ENTAE | Q99QC1)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        Q99QC1_ENTAE | Q99QC1: 5k1d 5k1f
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(-) Related Entries Specified in the PDB File

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