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(-) Description

Title :  CRYSTAL STRUCTURE OF FLUOROPHORE-LABELED BETA-LACTAMASE PENP
 
Authors :  W. -T. Wong, Y. -X. Zhao, Y. -C. Leung
Date :  16 Jun 11  (Deposition) - 27 Jul 11  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Lactamase, Fluorophore, Beta-Lactam, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. -T. Wong, K. -C. Chan, P. -K. So, H. -K. Yap, W. -H. Chung, Y. -C. Leung, K. -Y. Wong, Y. -X. Zhao
Increased Structural Flexibility At The Active Site Of A Fluorophore-Conjugated Beta-Lactamase Distinctively Impacts Its Binding Toward Diverse Cephalosporin Antibiotics
J. Biol. Chem. V. 286 31771 2011
PubMed-ID: 21705325  |  Reference-DOI: 10.1074/JBC.M110.198895

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SMALL EXOPENICILLINASE
    Gene: PENP
    Mutation: YES
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 1402
    Synonym: PENICILLINASE

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1BB02Ligand/Ion1-[6-(DIMETHYLAMINO)NAPHTHALEN-2-YL]ETHANONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BB01Ligand/Ion1-[6-(DIMETHYLAMINO)NAPHTHALEN-2-YL]ETHANONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BB01Ligand/Ion1-[6-(DIMETHYLAMINO)NAPHTHALEN-2-YL]ETHANONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:104 , ASN A:132 , CYS A:166 , LEU A:169 , ALA A:237 , HOH A:460BINDING SITE FOR RESIDUE BB0 A 2
2AC2SOFTWAREASN B:104 , CYS B:166 , LEU B:169BINDING SITE FOR RESIDUE BB0 B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SH7)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Pro A:167 -Glu A:168
2Asn A:170 -Glu A:171
3Glu A:171 -Val A:172
4Val A:172 -Asn A:173
5Pro A:174 -Gly A:175
6Leu B:169 -Asn B:170
7Val B:172 -Asn B:173
8Asn B:173 -Pro B:174
9Leu B:290 -Asn B:291

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SH7)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLAC_BACLI82-97
 		  2A:66-81
B:66-81
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLAC_BACLI82-97
 		  1A:66-81
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLAC_BACLI82-97
 		  1-
B:66-81

(-) Exons   (0, 0)

(no "Exon" information available for 3SH7)

(-) 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:257
 aligned with BLAC_BACLI | P00808 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:257
                                    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       
           BLAC_BACLI    47 KDDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 303
               SCOP domains d3sh7a_ A: beta-Lactamase, class A                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhh..hhhhh.ee..hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------BETA_LACTAMASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sh7 A  30 KDDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFCPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 291
                                    39        49       |60        70        80  ||    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     ||243       254       264       274       284       
                                                      57|                      83|                                                                                                                                                     238|         252|                                     
                                                       59                       86                                                                                                                                                      240          254                                     


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with BLAC_BACLI | P00808 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:255
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298     
           BLAC_BACLI    49 DFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 303
               SCOP domains d3sh7b_ B: beta-Lactamase, class A                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhhhhhhhh.ee..hhhhh.....hhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------BETA_LACTAMASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sh7 B  32 DFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFCPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 291
                                    41        51     || 62        72        82||      94       104       114       124       134       144       154       164       174       184       194       204       214       224       234   ||  245      |256       266       276       286     
                                                    57|                      83|                                                                                                                                                     238|         252|                                     
                                                     59                       86                                                                                                                                                      240          254
   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  (0, 0)

(no "CATH Domain" information available for 3SH7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SH7)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BLAC_BACLI | P00808)
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:0030655    beta-lactam antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  3.5.2.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        BLAC_BACLI | P00808: 1i2s 1i2w 1mbl 1w7f 2blm 2wk0 2y91 3b3x 3ly3 3ly4 3m2j 3m2k 3sh8 3sh9 3soi 4blm 4m3k 4n1h 4n92 4n9k 4n9l 5ghx 5ghy 5ghz

(-) Related Entries Specified in the PDB File

3sh8 3sh9