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(-) Description

Title :  CRYSTAL STRUCTURE OF A RATIONALLY DESIGNED OXA-10 VARIANT SHOWING CARBAPENEMASE ACTIVITY, OXA-10LOOP48
 
Authors :  F. De Luca, M. Benvenuti, F. Carboni, C. Pozzi, G. M. Rossolini, S. Mang J. D. Docquier
Date :  08 Feb 11  (Deposition) - 02 Nov 11  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antibiotic Resistance, Hydrolysis Of Amide Bond Of Beta-Lactam Compounds, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. De Luca, M. Benvenuti, F. Carboni, C. Pozzi, G. M. Rossolini, S. Mangani, J. D. Docquier
Evolution To Carbapenem-Hydrolyzing Activity In Noncarbapenemase Class D {Beta}-Lactamase Oxa-10 By Rationa Protein Design.
Proc. Natl. Acad. Sci. Usa V. 108 18424 2011
PubMed-ID: 22042844  |  Reference-DOI: 10.1073/PNAS.1110530108

(-) Compounds

Molecule 1 - OXACILLINASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLB-II-OXA10LOOP48
    Expression System Strain: DH5(ALPHA)
    Expression System Taxid: 668369
    Expression System Vector Type: PLB-II
    Fragment: SEE REMARK 999
    Gene: BLAOXA-10(LOOP48)
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 668369
    Synonym: OXA-10LOOP48, OXA-10 LABORATORY VARIANT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
1CO21Ligand/IonCARBON DIOXIDE
2EDO8Ligand/Ion1,2-ETHANEDIOL
3KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4SO49Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:13 , SER A:67 , SER A:115 , LYS A:205 , THR A:206 , GLY A:207 , TYR A:208 , ARG A:250 , HOH A:402 , HOH A:420 , HOH A:423 , HOH A:473BINDING SITE FOR RESIDUE SO4 A 1
02AC2SOFTWARESER B:67 , SER B:115 , LYS B:205 , THR B:206 , GLY B:207 , TYR B:208 , ARG B:250 , HOH B:280 , HOH B:379 , HOH B:428BINDING SITE FOR RESIDUE SO4 B 2
03AC3SOFTWAREARG B:131 , LYS B:134 , TYR B:135 , HOH B:446 , HOH B:499BINDING SITE FOR RESIDUE SO4 B 3
04AC4SOFTWARELYS A:134 , LYS A:138 , LYS A:152BINDING SITE FOR RESIDUE SO4 A 4
05AC5SOFTWAREGLY A:20 , LYS A:49 , HOH A:313BINDING SITE FOR RESIDUE SO4 A 5
06AC6SOFTWAREARG B:160 , HOH B:473BINDING SITE FOR RESIDUE SO4 B 6
07AC7SOFTWAREARG A:160 , HOH A:408 , HOH A:412 , HOH A:493BINDING SITE FOR RESIDUE SO4 A 7
08AC8SOFTWAREHOH A:12 , VAL A:130 , LEU A:155 , THR A:210 , ARG A:211 , HOH A:474 , HOH A:524 , HOH A:541 , HOH A:549BINDING SITE FOR RESIDUE SO4 A 8
09AC9SOFTWAREGLU A:227 , LYS A:228 , GLU A:229 , HOH A:521 , THR B:107 , ARG B:109 , GLY B:110BINDING SITE FOR RESIDUE SO4 A 9
10BC1SOFTWARETHR A:107 , ARG A:109 , GLU B:227 , GLU B:229BINDING SITE FOR RESIDUE EDO A 267
11BC2SOFTWAREASN A:176 , LYS A:182 , HOH A:448 , HOH A:479 , ASN B:85 , GLU B:86 , HIS B:87BINDING SITE FOR RESIDUE EDO A 2
12BC3SOFTWARELYS A:182 , HOH A:299 , HOH A:538BINDING SITE FOR RESIDUE EDO A 3
13BC4SOFTWAREGLY B:128 , GLU B:129 , VAL B:130 , HOH B:278 , HOH B:413BINDING SITE FOR RESIDUE EDO B 4
14BC5SOFTWAREASN B:38 , ARG B:58 , LYS B:61 , HOH B:321 , HOH B:324 , HOH B:394BINDING SITE FOR RESIDUE EDO B 5
15BC6SOFTWARETYR A:63 , LEU A:64 , ARG A:160 , GLU A:213 , PRO A:217 , HOH A:306 , HOH A:471BINDING SITE FOR RESIDUE EDO A 6
16BC7SOFTWAREPRO A:96 , ASN A:143 , GLN A:144 , HOH A:321BINDING SITE FOR RESIDUE EDO A 268
17BC8SOFTWARELYS A:100 , SER A:147 , GLY A:148 , GLY A:149 , HOH A:314BINDING SITE FOR RESIDUE EDO A 269
18BC9SOFTWAREARG A:58 , LYS A:61 , TYR A:63 , PRO A:217 , ASP A:240 , HOH A:287 , HOH A:503BINDING SITE FOR RESIDUE CO2 A 270

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:44 -A:51
2B:44 -B:51

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:213 -Pro A:217
2Glu B:213 -Pro B:217

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QNC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QNC)

(-) Exons   (0, 0)

(no "Exon" information available for 3QNC)

(-) 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:242
 aligned with Q7BNC2_ECOLX | Q7BNC2 from UniProtKB/TrEMBL  Length:266

    Alignment length:245
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259     
         Q7BNC2_ECOLX    20 GSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhh....eeeeeee....eeee.hhhhhh.ee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh...eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeeee-....--..eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qnc A  20 GSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGYS-TRIE--PKIGWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
                                    29        39        49        59        69|       79        89        99       109       119       129       139       149       159       169       179       189       199       209 |  |  219       229       239       249       259     
                                                                             70-KCX                                                                                                                                    209 |  |  |                                               
                                                                                                                                                                                                                         210  |  |                                               
                                                                                                                                                                                                                            213  |                                               
                                                                                                                                                                                                                               217                                               


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with Q7BNC2_ECOLX | Q7BNC2 from UniProtKB/TrEMBL  Length:266

    Alignment length:246
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259      
         Q7BNC2_ECOLX    20 GSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee...hhhhhhh....eeeeeee....eeee.hhhhhh.ee.hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeeee-....--.eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qnc B  20 GSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGYS-TRIE--PKIGWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
                                    29        39        49        59        69|       79        89        99       109       119       129       139       149       159       169       179       189       199       209 |  |  219       229       239       249       259      
                                                                             70-KCX                                                                                                                                    209 |  |  |                                                
                                                                                                                                                                                                                         210  |  |                                                
                                                                                                                                                                                                                            213  |                                                
                                                                                                                                                                                                                               217
   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 3QNC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QNC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QNC)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7BNC2_ECOLX | Q7BNC2)
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.
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
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.

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 Related Entries

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        Q7BNC2_ECOLX | Q7BNC2: 3qnb

(-) Related Entries Specified in the PDB File

3qnb