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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-10 AT 1.6 A RESOLUTION
 
Authors :  F. Kerff, E. Fonze, F. Bouillene, J. M. Frere, P. Charlier
Date :  08 Oct 01  (Deposition) - 31 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Lactamase, Hydrolase, Class D, Carbamylated Lysine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Kerff, E. Fonze, F. Bouillene, J. M. Frere, P. Charlier
Structure Of The Class D Beta-Lactamase Oxa-2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE PSE-2
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PLASMID PMON234
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: BETA LACTAMASE OXA-10

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:160 , HOH A:860 , HOH A:872 , HOH A:900 , HOH A:904 , HOH B:850BINDING SITE FOR RESIDUE SO4 A 701
2AC2SOFTWARESER A:67 , SER A:115 , LYS A:205 , THR A:206 , GLY A:207 , PHE A:208 , ARG A:250 , HOH A:847 , HOH A:905 , HOH A:1000BINDING SITE FOR RESIDUE SO4 A 702
3AC3SOFTWARESER B:67 , SER B:115 , LYS B:205 , THR B:206 , GLY B:207 , PHE B:208 , ARG B:250BINDING SITE FOR RESIDUE SO4 B 703
4AC4SOFTWAREARG B:160 , HOH B:905 , HOH B:924BINDING SITE FOR RESIDUE SO4 B 704

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K4F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K4F)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_DPS00337 Beta-lactamase class-D active site.BLO10_PSEAI65-75
 		  2A:65-75
B:65-75

(-) Exons   (0, 0)

(no "Exon" information available for 1K4F)

(-) 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:244
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:244
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
          BLO10_PSEAI    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
               SCOP domains d1k4fa_ A: Class D beta-lactamase                                                                                                                                                                                                                    SCOP domains
               CATH domains 1k4fA00 A:21-264 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhh....eeeeeee.....eee.hhhhhh....hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------BETA_LACTAM--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k4f A  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
                                                                            70-KCX                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:247
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       
          BLO10_PSEAI    19 AGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
               SCOP domains d1k4fb_ B: Class D beta-lactamase                                                                                                                                                                                                                       SCOP domains
               CATH domains 1k4fB00 B:19-265 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhh...eeeeeee....eeee.hhhhhhh...hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------BETA_LACTAM---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k4f B  19 MGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
                                    28        38        48        58        68 |      78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       
                                                                              70-KCX
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1K4F)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BLO10_PSEAI | P14489)
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

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

UniProtKB/Swiss-Prot
        BLO10_PSEAI | P14489: 1e3u 1e4d 1ewz 1fof 1k4e 1k54 1k55 1k56 1k57 1k6r 1k6s 2hp5 2hp6 2hp9 2hpb 2rl3 2wgi 2wgv 2wgw 2wkh 2wki 2x01 2x02 3lce 4s2o 4wz5 5fq9 5mmy 5mnu 5mox 5moz

(-) Related Entries Specified in the PDB File

1e4d STRUCTURE OF OXA10 BETA-LACTAMASE AT PH 8.3 AND 1.8 A RESOLUTION
1fof CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-10 AT 2 A RESOLUTION
1k4e CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASES OXA-10 DETERMINED BY MAD PHASING WITH SELENOMETHIONINE