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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CLOSED FORM OF PSEUDOMONAS AERUGINOSA SPM-1
 
Authors :  M. A. Mcdonough, J. Brem, C. J. Schofield
Date :  22 May 13  (Deposition) - 18 Jun 14  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Hydrolase, Metallo Beta Lactamase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Brem, W. B. Struwe, A. M. Rydzik, H. Tarhonskaya, I. Pfeffer, E. Flashman, S. S. Van Berkel, J. Spencer, T. D. W. Claridge, M. A. Mcdonough, J. L. P. Benesch, C. J. Schofield
Studying The Active-Site Loop Movement Of The Sao Paolo Metallo-Beta-Lactamase-1
Chem. Sci. V. 6 956 2015
PubMed-ID: 25717359  |  Reference-DOI: 10.1039/C4SC01752H

(-) Compounds

Molecule 1 - METALLO-B-LACTAMASE
    Chains: A, B, C, D
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: POPINF
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 29-276
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Strain: 48-1997A
    Synonym: SPM-1, METALLO-BETA-LACTAMASE BLASPM-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 25)

Asymmetric Unit (3, 25)
No.NameCountTypeFull Name
1CL7Ligand/IonCHLORIDE ION
2GOL8Ligand/IonGLYCEROL
3ZN10Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:108 , HIS A:110 , HIS A:197 , ZN A:1313 , HOH A:2056BINDING SITE FOR RESIDUE ZN A1312
02AC2SOFTWAREASP A:112 , CYS A:216 , HIS A:258 , ZN A:1312 , CL A:1318 , HOH A:2056BINDING SITE FOR RESIDUE ZN A1313
03AC3SOFTWAREHIS A:33 , ASP A:35 , HIS C:33 , ASP C:35BINDING SITE FOR RESIDUE ZN A1314
04AC4SOFTWAREHIS B:108 , HIS B:110 , HIS B:197 , ZN B:1312 , HOH B:2028BINDING SITE FOR RESIDUE ZN B1311
05AC5SOFTWAREASP B:112 , CYS B:216 , HIS B:258 , ZN B:1311 , CL B:1315 , HOH B:2028BINDING SITE FOR RESIDUE ZN B1312
06AC6SOFTWAREHIS B:33 , ASP B:35 , HIS D:33 , ASP D:35BINDING SITE FOR RESIDUE ZN B1313
07AC7SOFTWAREHIS C:108 , HIS C:110 , HIS C:197 , ZN C:1311 , HOH C:2029BINDING SITE FOR RESIDUE ZN C1310
08AC8SOFTWAREASP C:112 , CYS C:216 , HIS C:258 , ZN C:1310 , CL C:1314 , HOH C:2029BINDING SITE FOR RESIDUE ZN C1311
09AC9SOFTWAREHIS D:108 , HIS D:110 , HIS D:197 , ZN D:1311 , HOH D:2027BINDING SITE FOR RESIDUE ZN D1310
10BC1SOFTWAREASP D:112 , CYS D:216 , HIS D:258 , ZN D:1310 , CL D:1315 , HOH D:2027BINDING SITE FOR RESIDUE ZN D1311
11BC2SOFTWAREPRO D:37 , TYR D:38BINDING SITE FOR RESIDUE GOL D1312
12BC3SOFTWAREHIS A:110 , LEU A:111 , CL A:1317 , HOH A:2057 , HOH A:2084 , HOH A:2175 , HOH A:2176BINDING SITE FOR RESIDUE GOL A1315
13BC4SOFTWAREARG D:55BINDING SITE FOR RESIDUE GOL D1313
14BC5SOFTWAREPHE C:192 , GLY C:194BINDING SITE FOR RESIDUE GOL C1313
15BC6SOFTWAREHIS D:110 , LEU D:111 , ARG D:137 , GLU D:140 , HOH D:2041BINDING SITE FOR RESIDUE GOL D1314
16BC7SOFTWARELYS B:176 , PRO B:193 , ARG B:243BINDING SITE FOR RESIDUE GOL B1314
17BC8SOFTWAREPHE A:192 , GLY A:194BINDING SITE FOR RESIDUE GOL A1316
18BC9SOFTWAREARG A:137 , GOL A:1315 , HOH A:2091 , HOH A:2176BINDING SITE FOR RESIDUE CL A1317
19CC1SOFTWAREHIS C:197 , CYS C:216 , LYS C:219 , HIS C:258 , ZN C:1311 , HOH C:2029BINDING SITE FOR RESIDUE CL C1314
20CC2SOFTWAREHIS B:197 , CYS B:216 , LYS B:219 , HIS B:258 , ZN B:1312BINDING SITE FOR RESIDUE CL B1315
21CC3SOFTWAREHIS B:110 , LEU B:111BINDING SITE FOR RESIDUE CL B1316
22CC4SOFTWAREHIS D:197 , CYS D:216 , LYS D:219 , HIS D:258 , ZN D:1311BINDING SITE FOR RESIDUE CL D1315
23CC5SOFTWAREHIS A:197 , CYS A:216 , LYS A:219 , HIS A:258 , ZN A:1313 , HOH A:2056BINDING SITE FOR RESIDUE CL A1318

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BP0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BP0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BP0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BP0)

(-) Exons   (0, 0)

(no "Exon" information available for 4BP0)

(-) 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:246
 aligned with Q8G9Q0_PSEAI | Q8G9Q0 from UniProtKB/TrEMBL  Length:276

    Alignment length:246
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      
         Q8G9Q0_PSEAI    31 SDHVDLPYNLTATKIDSDVFVVTDRDFYSSNVLVAKMLDGTVVIVSSPFENLGTQTLMDWVAKTMKPKKVVAINTHFHLDGTGGNEIYKKMGAETWSSDLTKQLRLEENKKDRIKAAEFYKNEDLKRRILSSHPVPADNVFDLKQGKVFSFSNELVEVSFPGPAHSPDNVVVYFPKKKLLFGGCMIKPKELGYLGDANVKAWPDSARRLKKFDAKIVIPGHGEWGGPEMVNKTIKVAEKAVGEMRL 276
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee....eeeeeee..eeeeee.....eeeeeee....eeeee....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhh......eee.....eeeee..eeeeee...........eeee....eeeeehhh..............hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bp0 A  31 SDHVDLPYNLTATKIDSDVFVVTDRDFYSSNVLVAKMLDGTVVIVSSPFENLGTQTLMDWVAKTMKPKKVVAINTHFHLDGTGGNEIYKKMGAETWSSDLTKQLRLEENKKDRIKAAEFYKNEDLKRRILSSHPVPADNVFDLKQGKVFSFSNELVEVSFPGPAHSPDNVVVYFPKKKLLFGGCMIKPKELGYLGDANVKAWPDSARRLKKFDAKIVIPGHGEWGGPEMVNKTIKVAEKAVGEMRL 311
                                    40        50        60        70        80        90 ||    102       112       122       132       142       152       162       172       182       192       202       212       225       235       245 ||    257   ||  295       305      
                                                                                        92|                                                                                                                          220|                    247|        261|                     
                                                                                         95                                                                                                                           224                     250         290                     


Chain B from PDB  Type:PROTEIN  Length:245
 aligned with Q8G9Q0_PSEAI | Q8G9Q0 from UniProtKB/TrEMBL  Length:276

    Alignment length:245
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     
         Q8G9Q0_PSEAI    31 SDHVDLPYNLTATKIDSDVFVVTDRDFYSSNVLVAKMLDGTVVIVSSPFENLGTQTLMDWVAKTMKPKKVVAINTHFHLDGTGGNEIYKKMGAETWSSDLTKQLRLEENKKDRIKAAEFYKNEDLKRRILSSHPVPADNVFDLKQGKVFSFSNELVEVSFPGPAHSPDNVVVYFPKKKLLFGGCMIKPKELGYLGDANVKAWPDSARRLKKFDAKIVIPGHGEWGGPEMVNKTIKVAEKAVGEMR 275
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeee..eeeeee.....eeeeeee....eeeee....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh..hhhhhhh...hhhhhhhhhhh......eee.....eeeee..eeeeee...........eeeehhh.eeeeehhh..............hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bp0 B  31 SDHVDLPYNLTATKIDSDVFVVTDRDFYSSNVLVAKMLDGTVVIVSSPFENLGTQTLMDWVAKTMKPKKVVAINTHFHLDGTGGNEIYKKMGAETWSSDLTKQLRLEENKKDRIKAAEFYKNEDLKRRILSSHPVPADNVFDLKQGKVFSFSNELVEVSFPGPAHSPDNVVVYFPKKKLLFGGCMIKPKELGYLGDANVKAWPDSARRLKKFDAKIVIPGHGEWGGPEMVNKTIKVAEKAVGEMR 310
                                    40        50        60        70        80        90 ||    102       112       122       132       142       152       162       172       182       192       202       212       225       235       245 ||    257   ||  295       305     
                                                                                        92|                                                                                                                          220|                    247|        261|                    
                                                                                         95                                                                                                                           224                     250         290                    


Chain C from PDB  Type:PROTEIN  Length:244
 aligned with Q8G9Q0_PSEAI | Q8G9Q0 from UniProtKB/TrEMBL  Length:276

    Alignment length:244
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    
         Q8G9Q0_PSEAI    31 SDHVDLPYNLTATKIDSDVFVVTDRDFYSSNVLVAKMLDGTVVIVSSPFENLGTQTLMDWVAKTMKPKKVVAINTHFHLDGTGGNEIYKKMGAETWSSDLTKQLRLEENKKDRIKAAEFYKNEDLKRRILSSHPVPADNVFDLKQGKVFSFSNELVEVSFPGPAHSPDNVVVYFPKKKLLFGGCMIKPKELGYLGDANVKAWPDSARRLKKFDAKIVIPGHGEWGGPEMVNKTIKVAEKAVGEM 274
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeeeeee..eeeeee.....eeeeeee....eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh..hhhhhhh...hhhhhhhhhhh......eee.....eeeee..eeeeee...........eeee....eeeeehhh..............hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bp0 C  31 SDHVDLPYNLTATKIDSDVFVVTDRDFYSSNVLVAKMLDGTVVIVSSPFENLGTQTLMDWVAKTMKPKKVVAINTHFHLDGTGGNEIYKKMGAETWSSDLTKQLRLEENKKDRIKAAEFYKNEDLKRRILSSHPVPADNVFDLKQGKVFSFSNELVEVSFPGPAHSPDNVVVYFPKKKLLFGGCMIKPKELGYLGDANVKAWPDSARRLKKFDAKIVIPGHGEWGGPEMVNKTIKVAEKAVGEM 309
                                    40        50        60        70        80        90 ||    102       112       122       132       142       152       162       172       182       192       202       212       225       235       245 ||    257   ||  295       305    
                                                                                        92|                                                                                                                          220|                    247|        261|                   
                                                                                         95                                                                                                                           224                     250         290                   


Chain D from PDB  Type:PROTEIN  Length:244
 aligned with Q8G9Q0_PSEAI | Q8G9Q0 from UniProtKB/TrEMBL  Length:276

    Alignment length:244
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    
         Q8G9Q0_PSEAI    31 SDHVDLPYNLTATKIDSDVFVVTDRDFYSSNVLVAKMLDGTVVIVSSPFENLGTQTLMDWVAKTMKPKKVVAINTHFHLDGTGGNEIYKKMGAETWSSDLTKQLRLEENKKDRIKAAEFYKNEDLKRRILSSHPVPADNVFDLKQGKVFSFSNELVEVSFPGPAHSPDNVVVYFPKKKLLFGGCMIKPKELGYLGDANVKAWPDSARRLKKFDAKIVIPGHGEWGGPEMVNKTIKVAEKAVGEM 274
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeeeeee..eeeeee.....eeeeeee....eeeee....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh.hhhhhhh...hhhhhhhhhh.......eee.....eeeee..eeeeee...........eeee....eeeeehhh..............hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bp0 D  31 SDHVDLPYNLTATKIDSDVFVVTDRDFYSSNVLVAKMLDGTVVIVSSPFENLGTQTLMDWVAKTMKPKKVVAINTHFHLDGTGGNEIYKKMGAETWSSDLTKQLRLEENKKDRIKAAEFYKNEDLKRRILSSHPVPADNVFDLKQGKVFSFSNELVEVSFPGPAHSPDNVVVYFPKKKLLFGGCMIKPKELGYLGDANVKAWPDSARRLKKFDAKIVIPGHGEWGGPEMVNKTIKVAEKAVGEM 309
                                    40        50        60        70        80        90 ||    102       112       122       132       142       152       162       172       182       192       202       212       225       235       245 ||    257   ||  295       305    
                                                                                        92|                                                                                                                          220|                    247|        261|                   
                                                                                         95                                                                                                                           224                     250         290
   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  (0, 0)

(no "SCOP Domain" information available for 4BP0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BP0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BP0)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8G9Q0_PSEAI | Q8G9Q0)
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.

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  4bp0
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  Q8G9Q0_PSEAI | Q8G9Q0
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 Related Entries

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

UniProtKB/TrEMBL
        Q8G9Q0_PSEAI | Q8G9Q0: 2fhx 5ls3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4BP0)