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(-) Description

Title :  STRUCTURE OF BETA-LACTAMASE II FROM BACILLUS CEREUS. R121H, C221S DOUBLE MUTANT. SPACE GROUP P3121.
 
Authors :  F. J. Medrano Martin, A. J. Vila, J. M. Gonzalez
Date :  23 Nov 06  (Deposition) - 29 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  B  (2x)
Keywords :  Beta-Lactamase Ii, Bacillus Cereus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Gonzalez, F. J. Medrano Martin, A. L. Costello, D. L. Tierney, A. J. Vila
The Zn2 Position In Metallo-Beta-Lactamases Is Critical For Activity: A Study On Chimeric Metal Sites On A Conserved Protein Scaffold.
J. Mol. Biol. V. 373 1141 2007
PubMed-ID: 17915249  |  Reference-DOI: 10.1016/J.JMB.2007.08.031

(-) Compounds

Molecule 1 - BETA-LACTAMASE II
    ChainsA, B
    EC Number3.5.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    GeneBLM
    MutationYES
    Organism ScientificBACILLUS CEREUS
    Organism Taxid1396
    SynonymPENICILLINASE, CEPHALOSPORINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (2x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric Unit (4, 19)
No.NameCountTypeFull Name
1ACY8Ligand/IonACETIC ACID
2GOL3Ligand/IonGLYCEROL
3SO46Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2GOL2Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2GOL1Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (3, 16)
No.NameCountTypeFull Name
1ACY8Ligand/IonACETIC ACID
2GOL2Ligand/IonGLYCEROL
3SO46Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:86 , HIS A:88 , HIS A:149 , HOH A:726 , HOH A:812BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREHIS B:86 , HIS B:88 , HIS B:149 , HOH B:785 , HOH B:816BINDING SITE FOR RESIDUE ZN B 402
03AC3SOFTWARESER A:172 , THR A:173 , SER A:174 , GLY A:211 , GLU A:212 , HOH A:773 , HOH A:845BINDING SITE FOR RESIDUE SO4 A 501
04AC4SOFTWARESER B:172 , THR B:173 , SER B:174 , GLY B:211 , GLU B:212 , HOH B:706BINDING SITE FOR RESIDUE SO4 B 502
05AC5SOFTWARELYS A:65 , GLU A:69 , ARG A:101 , ILE A:203 , LYS A:216 , HOH A:744 , HOH A:806BINDING SITE FOR RESIDUE SO4 A 503
06AC6SOFTWARELYS B:134 , LYS B:139 , ARG B:199BINDING SITE FOR RESIDUE SO4 B 504
07AC7SOFTWARESER A:168 , LYS A:171 , HIS A:210 , HOH A:750 , HOH A:765BINDING SITE FOR RESIDUE SO4 A 505
08AC8SOFTWARESER B:168 , LYS B:171 , GLY B:209 , HIS B:210 , HOH B:732 , HOH B:743 , HOH B:850BINDING SITE FOR RESIDUE SO4 B 506
09AC9SOFTWAREASP B:60 , ASP B:61 , LYS B:62BINDING SITE FOR RESIDUE ACY B 601
10BC1SOFTWARELYS A:99 , GLU A:121BINDING SITE FOR RESIDUE ACY A 602
11BC2SOFTWAREASN A:162BINDING SITE FOR RESIDUE ACY A 603
12BC3SOFTWARELYS B:99 , GLU B:121 , GLU B:122BINDING SITE FOR RESIDUE ACY B 604
13BC4SOFTWAREASN B:162 , ASN B:202BINDING SITE FOR RESIDUE ACY B 605
14BC5SOFTWAREALA B:175 , LYS B:176 , ASP B:177 , HOH B:854BINDING SITE FOR RESIDUE ACY B 606
15BC6SOFTWAREASP A:60 , ASP A:61 , LYS A:62BINDING SITE FOR RESIDUE ACY A 607
16BC7SOFTWAREALA A:175 , LYS A:176 , ASP A:177 , HOH A:873BINDING SITE FOR RESIDUE ACY A 608
17BC8SOFTWAREASN A:137 , LYS A:139 , GLN A:160 , HOH A:740BINDING SITE FOR RESIDUE GOL A 701
18BC9SOFTWAREALA A:182 , ASP A:183 , ALA A:184 , TYR A:185 , HOH A:832 , HOH A:874 , LYS B:227BINDING SITE FOR RESIDUE GOL A 702
19CC1SOFTWARETHR B:29 , ASN B:42 , GLY B:211 , GLU B:212 , VAL B:213 , HOH B:720 , HOH B:723 , HOH B:894BINDING SITE FOR RESIDUE GOL B 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NZE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NZE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NZE)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA2_BACCE113-132
 
  2A:83-102
B:83-102
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLA2_BACCE189-201
 
  2A:159-171
B:159-171
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA2_BACCE113-132
 
  1A:83-102
-
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLA2_BACCE189-201
 
  1A:159-171
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA2_BACCE113-132
 
  1-
B:83-102
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLA2_BACCE189-201
 
  1-
B:159-171
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA2_BACCE113-132
 
  2-
B:83-102
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLA2_BACCE189-201
 
  2-
B:159-171

(-) Exons   (0, 0)

(no "Exon" information available for 2NZE)

(-) 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:215
 aligned with BLA2_BACCE | P04190 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:221
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256 
           BLA2_BACCE    37 TVIKNETGTISISQLNKNVWVHTELGSFNGEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADRIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVPGHGEVGDKGLLLHTLDLLK 257
               SCOP domains d2nzea_ A: Zn metallo-beta      -lactamase                                                                                                                                                                                    SCOP domains
               CATH domains 2nzeA00 A:7-227 Metallo-be      ta-lactamase, chain A                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeeeeee..eeeeee..------..eeeeeeee..eeeee....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..eee.hhhhhhhhhhh...........eeeeee..eeeeee...........eee.....eeeeehhh..............hhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------BETA_LACTAMASE_B_1  --------------------------------------------------------BETA_LACTAMAS-------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nze A   7 TVIKNETGTISISQLNKNVWVHTELG------VPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADHIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGSLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVPGHGEVGDKGLLLHTLDLLK 227
                                    16        26     |   -  |     46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226 
                                                    32     39                                                                                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with BLA2_BACCE | P04190 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:222
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255  
           BLA2_BACCE    36 KTVIKNETGTISISQLNKNVWVHTELGSFNGEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADRIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVPGHGEVGDKGLLLHTLDLLK 257
               SCOP domains d2nzeb_ B: Zn metallo-beta-     lactamase                                                                                                                                                                                      SCOP domains
               CATH domains 2nzeB00 B:6-227 Metallo-bet     a-lactamase, chain A                                                                                                                                                                           CATH domains
           Pfam domains (1) --------------------------------Lactamase_B-2nzeB01 B:38-210                                                                                                                                                 ----------------- Pfam domains (1)
           Pfam domains (2) --------------------------------Lactamase_B-2nzeB02 B:38-210                                                                                                                                                 ----------------- Pfam domains (2)
         Sec.struct. author ..eee.....eeeeeee..eeeeeee.-----..eeeeeeeee..eeeee....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..eee.hhhhhhhhhhh...........eeeeee..eeeeee...........eee.....eeeeehhh..............hhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------BETA_LACTAMASE_B_1  --------------------------------------------------------BETA_LACTAMAS-------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nze B   6 KTVIKNETGTISISQLNKNVWVHTELG-----AVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADHIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGSLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVPGHGEVGDKGLLLHTLDLLK 227
                                    15        25      |  -  |     45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225  
                                                     32    38                                                                                                                                                                                             

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BLA2_BACCE | P04190)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        BLA2_BACCE | P041901bc2 1bmc 1bvt 1dxk 1mqo 2bc2 2bfk 2bfl 2bfz 2bg2 2bg6 2bg7 2bg8 2bga 2m5c 2m5d 2nxa 2nyp 2nzf 2uyx 3bc2 3fcz 3i0v 3i11 3i13 3i14 3i15 3knr 3kns 4c09 4c1c 4c1h 4nq4 4nq5 4nq6 4nq7 4tyt 5fqa 5fqb 5jmx 5w8w

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2NZE)