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(-) Description

Title :  GC1 BETA-LACTAMASE WITH A PENEM INHIBITOR
 
Authors :  M. Nukaga, K. Nukaga, J. R. Knox
Date :  27 Feb 03  (Deposition) - 09 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym./Biol. Unit :  A
Keywords :  Mixed Alpha/Beta, Cephalosporinase, Inhibition, Class C Beta- Lactamase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nukaga, T. Abe, A. M. Venkatesan, T. S. Mansour, R. A. Bonomo, J. R. Knox
Inhibition Of Class A And Class C Beta-Lactamases By Penems Crystallographic Structures Of A Novel 1, 4-Thiazepine Intermediate
Biochemistry V. 42 13152 2003
PubMed-ID: 14609325  |  Reference-DOI: 10.1021/BI034986B

(-) Compounds

Molecule 1 - CLASS C BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCS101
    Expression System Strain: AS226-51
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BLAC
    Organism Scientific: ENTEROBACTER CLOACAE
    Organism Taxid: 550

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2WY41Ligand/Ion7-(5,6-DIHYDRO-8H-IMIDAZO[2,1-C][1,4]OXAZIN-2-YL)-6-FORMYL-2,7-DIHYDRO- [1,4]THIAZEPINE-3-CARBOXYLIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:64 , LEU A:119 , GLN A:120 , ASN A:152 , GLY A:320 , SER A:321 , THR A:322 , GLY A:323 , GOL A:413 , HOH A:693 , HOH A:722 , HOH A:740 , HOH A:871BINDING SITE FOR RESIDUE WY4 A 400
2AC2SOFTWAREPRO A:181 , LEU A:182 , ASN A:245 , VAL A:246 , ALA A:247 , ASP A:248 , HOH A:768BINDING SITE FOR RESIDUE GOL A 410
3AC3SOFTWARELYS A:293 , VAL A:294 , ALA A:297 , HOH A:652BINDING SITE FOR RESIDUE GOL A 411
4AC4SOFTWARESER A:290 , ASP A:291 , SER A:292 , PRO A:348 , ASN A:349 , PRO A:350 , HOH A:663 , HOH A:872 , HOH A:891BINDING SITE FOR RESIDUE GOL A 412
5AC5SOFTWAREARG A:210 , ALA A:211 , VAL A:212 , THR A:322 , GLY A:323 , WY4 A:400 , HOH A:562BINDING SITE FOR RESIDUE GOL A 413

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:279 -Pro A:280
2Asn A:305 -Pro A:306

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ONH)

(-) 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:363
 aligned with Q59401_ENTCL | Q59401 from UniProtKB/TrEMBL  Length:384

    Alignment length:363
                                    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       281       291       301       311       321       331       341       351       361       371       381   
         Q59401_ENTCL    22 PVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ 384
               SCOP domains d1onha_ A: AMPC beta-Lactamase, class C                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1onhA00 A:2-364 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ----------Beta-lactamase-1onhA01 A:12-364                                                                                                                                                                                                                                                                                                                                   Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhh.....hhhhh..hhhhhhhh..............hhhhhhhhhhhh........ee..hhhhhhhhhhhhh.....hhhhhhhhhh........ee...hhhhhhhh..eee..eee.........hhhhhhh.eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhhhhhhhhhh..ee.eeeeeee.....eeeeeeee....eeeeeee....eeeeeee....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1onh A   2 PVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ 364
                                    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       281       291       301       311       321       331       341       351       361
   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   (Q59401_ENTCL | Q59401)
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/TrEMBL
        Q59401_ENTCL | Q59401: 1ga0 1q2q

(-) Related Entries Specified in the PDB File

1gao GC1 BETA-LACTAMASE WITH A SULFONE INHIBITOR
1gce BETA-LACTAMASE (UNLIGANDED) OF ENTEROBACTER CLOACAE GC1
1ong SHV-1 BETA-LACTAMASE WITH A PENEM INHIBITOR