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(-) Description

Title :  ULTRAHIGH RESOLUTION STRUCTURE OF A CLASS A BETA-LACTAMASE: ON THE MECHANISM AND SPECIFICITY OF THE EXTENDED-SPECTRUM SHV-2 ENZYME
 
Authors :  M. Nukaga, K. Mayama, A. M. Hujer, R. A. Bonomo, J. R. Knox
Date :  22 Nov 02  (Deposition) - 08 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Lactam Hydrolase, Penicillinase, Detergent Binding, Drug Design, Radiation Damage (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nukaga, K. Mayama, A. M. Hujer, R. A. Bonomo, J. R. Knox
Ultrahigh Resolution Structure Of A Class A Beta-Lactamase: On The Mechanism And Specificity Of The Extended-Spectrum Shv-2 Enzyme
J. Mol. Biol. V. 328 289 2003
PubMed-ID: 12684014  |  Reference-DOI: 10.1016/S0022-2836(03)00210-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE SHV-2
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI STR. K-12 SUBSTR. DH10B
    Expression System Gene: BLA
    Expression System Plasmid: PBCSK
    Expression System Strain: DH10B
    Expression System Taxid: 316385
    Expression System Vector Type: PLASMID
    Gene: BLA
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Synonym: PENICILLINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2MA42Ligand/IonCYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:93 , HIS A:96 , ARG A:98 , VAL A:224 , LEU A:225 , PRO A:226 , ILE A:246 , ALA A:248 , VAL A:261 , ILE A:263 , ALA A:280 , ALA A:284 , GLU A:288 , HOH A:505 , HOH A:544 , HOH A:596 , HOH A:621 , HOH A:626 , HOH A:688BINDING SITE FOR RESIDUE MA4 A 300
2AC2SOFTWAREARG A:244 , ILE A:246 , ILE A:279BINDING SITE FOR RESIDUE MA4 A 310
3AC3SOFTWARESER A:70 , TYR A:105 , SER A:130 , VAL A:216 , LYS A:234 , THR A:235 , GLY A:236 , ALA A:237 , ARG A:244 , HOH A:515 , HOH A:716BINDING SITE FOR RESIDUE EPE A 400
4AC4SOFTWAREALA A:82 , GLN A:154 , ASP A:176 , ARG A:198 , HOH A:587 , HOH A:592 , HOH A:652 , HOH A:791BINDING SITE FOR RESIDUE MPD A 500

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:77 -A:123

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:166 -Thr A:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N9B)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLA3_KLEPN62-77  1A:66-81

(-) Exons   (0, 0)

(no "Exon" information available for 1N9B)

(-) 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:265
 aligned with BLA3_KLEPN | P30896 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:265
                                    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     
           BLA3_KLEPN    22 SPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQLQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR 286
               SCOP domains d1n9ba_ A: beta-Lactamase, class A                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1n9bA00 A:26-292 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------Beta-lactamase2-1n9bA01 A:51-263                                                                                                                                                                                   ----------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh.....hhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhh......eeeeeeeee...eeeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------BETA_LACTAMASE_A----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n9b A  26 SPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR 292
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287     
                                                                                                                                                                                                                                              238|         252|                                      
                                                                                                                                                                                                                                               240          254
   Legend:   → Mismatch (orange background)
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  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  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BLA3_KLEPN | P30896)
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.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1htz STRUCTURE OF THE TEM-52 BETA-LACTAMASE
1shv STRUCTURE OF THE SHV-1 BETA-LACTAMASE