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(-) Description

Title :  ZINC-BETA-LACTAMASE L1 FROM STENOTROPHOMONAS MALTOPHILIA (MP2 INHIBITOR COMPLEX)
 
Authors :  L. Nauton, G. Garau, R. Kahn, O. Dideberg
Date :  26 Jan 06  (Deposition) - 30 Jan 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)
Keywords :  Hydrolase, Zn, Metallo, Beta, Lactamase, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Nauton, R. Kahn, G. Garau, J. F. Hernandez, O. Dideberg
Structural Insights Into The Design Of Inhibitors For The L Metallo-Beta-Lactamase From Stenotrophomonas Maltophilia.
J. Mol. Biol. V. 375 257 2008
PubMed-ID: 17999929  |  Reference-DOI: 10.1016/J.JMB.2007.10.036
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE L1
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: L1
    Organism Scientific: STENOTROPHOMONAS MALTOPHILIA
    Organism Taxid: 40324
    Synonym: BETA-LACTAMASE TYPE II, 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  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MP22Ligand/IonN-[(BENZYLOXY)CARBONYL]-L-CYSTEINYLGLYCINE
3SO47Ligand/IonSULFATE ION
4ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MP21Ligand/IonN-[(BENZYLOXY)CARBONYL]-L-CYSTEINYLGLYCINE
3SO45Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MP21Ligand/IonN-[(BENZYLOXY)CARBONYL]-L-CYSTEINYLGLYCINE
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:116 , HIS A:118 , HIS A:196 , MP2 A:1410BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREASP A:120 , HIS A:121 , HIS A:263 , MP2 A:1410 , HOH A:1641BINDING SITE FOR RESIDUE ZN A 402
03AC3SOFTWAREHIS B:116 , HIS B:118 , HIS B:196 , MP2 B:2410BINDING SITE FOR RESIDUE ZN B 401
04AC4SOFTWAREASP B:120 , HIS B:121 , HIS B:263 , MP2 B:2410 , HOH B:2580BINDING SITE FOR RESIDUE ZN B 402
05AC5SOFTWAREARG B:172 , VAL B:179 , ILE B:180 , THR B:181 , HOH B:2479 , HOH B:2573BINDING SITE FOR RESIDUE SO4 B 1
06AC6SOFTWAREARG A:172 , VAL A:179 , ILE A:180 , THR A:181 , HOH A:1587 , HOH A:1687 , HOH A:1716BINDING SITE FOR RESIDUE SO4 A 2
07AC7SOFTWAREARG A:252 , LYS A:297 , HOH A:1518 , HOH A:1528 , ARG B:209 , ALA B:275 , ARG B:276 , ALA B:289 , GLY B:290 , ALA B:291BINDING SITE FOR RESIDUE SO4 A 3
08AC8SOFTWAREARG A:209 , ALA A:275 , ARG A:276 , ALA A:289 , GLY A:290 , ALA A:291 , HOH A:1543 , HOH A:1563 , ARG B:252 , LYS B:297BINDING SITE FOR RESIDUE SO4 A 4
09AC9SOFTWAREARG A:252 , HOH A:1721 , ARG B:209 , ASN B:210BINDING SITE FOR RESIDUE SO4 A 5
10BC1SOFTWAREARG A:102 , ASN A:210 , HOH A:1494 , HOH A:1549BINDING SITE FOR RESIDUE SO4 A 6
11BC2SOFTWAREARG B:102 , GLY B:211 , HOH B:2602BINDING SITE FOR RESIDUE SO4 B 7
12BC3SOFTWARETYR A:33 , TRP A:39 , ASP A:120 , PHE A:156 , GLY A:161 , ILE A:162 , HIS A:196 , SER A:225 , PRO A:227 , HIS A:263 , ZN A:401 , ZN A:402 , HOH A:1630 , HOH A:1641 , HOH A:1673BINDING SITE FOR RESIDUE MP2 A 1410
13BC4SOFTWARETYR B:33 , TRP B:39 , ASP B:120 , PHE B:156 , GLY B:161 , HIS B:196 , SER B:225 , ZN B:401 , ZN B:402 , HOH B:2508 , HOH B:2580 , HOH B:2587 , HOH B:2590 , HOH B:2616BINDING SITE FOR RESIDUE MP2 B 2410
14BC5SOFTWAREPHE A:248 , ALA A:249 , ALA A:300 , ASP A:301 , GLU A:304 , HOH A:1500 , HOH A:1603 , HOH A:1633 , HOH A:1655 , ARG B:276BINDING SITE FOR RESIDUE GOL A 8
15BC6SOFTWAREARG A:276 , ALA B:249 , ARG B:252 , ALA B:300 , ASP B:301 , GLU B:304 , HOH B:2490 , HOH B:2577 , HOH B:2662BINDING SITE FOR RESIDUE GOL B 9
16BC7SOFTWAREARG A:130 , HOH A:1480 , ARG B:148 , ASP B:152 , ASP B:171 , ARG B:172 , ILE B:173 , HOH B:2531 , HOH B:2571 , HOH B:2677BINDING SITE FOR RESIDUE GOL B 10
17BC8SOFTWAREHOH A:1470 , PRO B:166 , ALA B:168 , ASN B:169 , HOH B:2536BINDING SITE FOR RESIDUE GOL B 11

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:256 -A:296
2B:256 -B:296

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FU9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FU9)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA1_STEMA102-122
 		  2A:113-133
B:113-133
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA1_STEMA102-122
 		  1A:113-133
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA1_STEMA102-122
 		  1-
B:113-133

(-) Exons   (0, 0)

(no "Exon" information available for 2FU9)

(-) 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:266
 aligned with BLA1_STEMA | P52700 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:266
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      
           BLA1_STEMA    23 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 288
               SCOP domains d2fu9a_ A: Zn metallo-beta-lactamase                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2fu9A00 A:24-317 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh....eeee..eee........eeeee..eeeee...hhhhhhhhhhhhhhhh.hhh.eeeee....hhhhhhhhhhhhhhh..eeeehhhhhhhhhh....................ee.....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhh....eee..hhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------BETA_LACTAMASE_B_1   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fu9 A  24 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 317
                                    33        43        53   ||   72        82    ||  93       103       113       123       133       143       153   ||  165||     176       186    || 197       207       217    || 229       239       249       259       269      |291       301       311      
                                                            57|                  87|                                                                 157|   166|                    191|                          222|                                                276|                            
                                                             67                   89                                                                  160    168                     193                           225                                                 289                            


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with BLA1_STEMA | P52700 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:266
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      
           BLA1_STEMA    23 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 288
               SCOP domains d2fu9b_ B: Zn metallo-beta-lactamase                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2fu9B00 B:24-317 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh....eeee..eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhh..eeeehhhhhhhhhh....................ee.....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhh....eee..hhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------BETA_LACTAMASE_B_1   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fu9 B  24 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 317
                                    33        43        53   ||   72        82    ||  93       103       113       123       133       143       153   ||  165||     176       186    || 197       207       217    || 229       239       249       259       269      |291       301       311      
                                                            57|                  87|                                                                 157|   166|                    191|                          222|                                                276|                            
                                                             67                   89                                                                  160    168                     193                           225                                                 289
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FU9)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BLA1_STEMA | P52700)
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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  2fu9
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  BLA1_STEMA | P52700
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 Related Entries

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

UniProtKB/Swiss-Prot
        BLA1_STEMA | P52700: 1sml 2aio 2fm6 2fu6 2fu7 2fu8 2gfj 2gfk 2h6a 2hb9 2qdt 2qin 2qjs 5dpx 5evb 5evd 5evk 5hh5 5hh6

(-) Related Entries Specified in the PDB File

2fm6 2fu6 2fu7 2fu8