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(-) Description

Title :  NEUTRON STRUCTURE OF A PERDEUTERATED TOHO-1 R274N R276N DOUBLE MUTANT BETA-LACTAMASE IN COMPLEX WITH A FULLY DEUTERATED BORONIC ACID (BZB)
 
Authors :  S. J. Tomanicek, K. L. Weiss, R. F. Standaert, A. Ostermann, T. E. Schrad J. D. Ng, L. Coates
Date :  04 Oct 12  (Deposition) - 16 Jan 13  (Release) - 22 Mar 17  (Revision)
Method :  NEUTRON DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Keywords :  Hydrolase, Perdeuterated Neutron Structure, Extended-Spectrum Beta Lactamases, Ctx- M-Type Esbls (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Tomanicek, R. F. Standaert, K. L. Weiss, A. Ostermann, T. E. Schrader, J. D. Ng, L. Coates
Neutron And X-Ray Crystal Structures Of A Perdeuterated Enzyme Inhibitor Complex Reveal The Catalytic Proton Networ Of The Toho-1 Beta-Lactamase For The Acylation Reaction.
J. Biol. Chem. V. 288 4715 2013
PubMed-ID: 23255594  |  Reference-DOI: 10.1074/JBC.M112.436238

(-) Compounds

Molecule 1 - TOHO-1 BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI BL21
    Organism Taxid: 511693
    Other Details: PERDEUTERATED

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 146)

Asymmetric Unit (2, 146)
No.NameCountTypeFull Name
1BZB1Ligand/IonBENZO[B]THIOPHENE-2-BORONIC ACID
2DOD145Ligand/Ion
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BZB1Ligand/IonBENZO[B]THIOPHENE-2-BORONIC ACID
2DOD-1Ligand/Ion

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:70 , ASN A:104 , TYR A:105 , SER A:130 , ASN A:132 , GLY A:236 , SER A:237BINDING SITE FOR RESIDUE BZB A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BD1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:166 -Pro A:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BD1)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLT1_ECOLX69-84  1A:66-81
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLT1_ECOLX69-84  1A:66-81

(-) Exons   (0, 0)

(no "Exon" information available for 4BD1)

(-) Sequences/Alignments

Asymmetric Unit
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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:261
 aligned with BLT1_ECOLX | Q47066 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:261
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
           BLT1_ECOLX    31 NSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAERRRDILAAAAKIVTHGF 291
               SCOP domains d4bd1a_ A: beta-Lactamase, class A                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh...hhhh.eee.hhhhh......hhhhh..eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------BETA_LACTAMASE_A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bd1 A  27 NSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAENRNDILAAAAKIVTHGF 290
                                    36        46        56||      67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237||     248   ||  259       269       279       289 
                                                         57|                                                                                                                                                                                238|         252|                                    
                                                          59                                                                                                                                                                                 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 Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BD1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BD1)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (BLT1_ECOLX | Q47066)
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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  3.5.2.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        BLT1_ECOLX | Q47066: 1bza 1iyo 1iyp 1iyq 1iys 1we4 2wyx 2xqz 2xr0 2zq7 2zq8 2zq9 2zqa 2zqc 2zqd 4bd0 4c3q 4x69 5kmw 5ksc

(-) Related Entries Specified in the PDB File

1bza BETA-LACTAMASE TOHO-1 FROM ESCHERICHIA COLI TUH12191
1iyo TOHO-1 BETA-LACTAMASE IN COMPLEX WITH CEFOTAXIME
1iyp TOHO-1 BETA-LACTAMASE IN COMPLEX WITH CEPHALOTHIN
1iyq TOHO-1 BETA-LACTAMASE IN COMPLEX WITH BENZYLPENICILLIN
1iys CRYSTAL STRUCTURE OF CLASS A BETA-LACTAMASE TOHO-1
1we4 CRYSTAL STRUCTURE OF CLASS A BETA-LACTAMASE TOHO-1 G238CMUTANT
2wyx NEUTRON STRUCTURE OF A CLASS A BETA-LACTAMASE TOHO-1 E166A R274N R276N TRIPLE MUTANT
2xqz NEUTRON STRUCTURE OF THE PERDEUTERATED TOHO-1 R274N R276N DOUBLE MUTANT BETA-LACTAMASE
2xr0 ROOM TEMPERATURE X-RAY STRUCTURE OF THE PERDEUTERATED TOHO-1 R274N R276N DOUBLE MUTANT BETA-LACTAMASE
4bd0 X-RAY STRUCTURE OF A PERDEUTERATED TOHO-1 R274N R276N DOUBLE MUTANT BETA-LACTAMASE IN COMPLEX WITH A FULLY DEUTERATED BORONIC ACID (BZB)