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(-) Description

Title :  CRYSTAL STRUCTURE OF TEM-1 BETA-LACTAMASE IN COMPLEX WITH BORON-BASED INHIBITOR EC25
 
Authors :  E. Dellus-Gur, M. Elias, J. S. Fraser, D. S. Tawfik
Date :  09 Feb 14  (Deposition) - 20 May 15  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Beta-Lactamase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Dellus-Gur, M. Elias, E. Caselli, F. Prati, J. S. Fraser, D. S. Tawfi
Negative Epistasis In Enzyme Evolution The Thin Line Betwee Conformational Freedom And Anarchy
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMPICILLIN RESISTANCE PROTEIN
    Chains: A, B, C, D, E, F
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: TEM-1
    Gene: BLA, BLATEM-116
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: BETA LACTAMASE, BETA-LACTAMASE, BETALACTAMASE TEM-116, BLATEM, EXTENDED SPECTRUM BETA-LACTAMASE, MUTANT EXTENDED-SPECTRUM BETA-LACTAMASE, TEM EXTENDED SPECTRUM BETA-LACTAMASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
12UL5Ligand/Ion3-[(2R)-2-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}-2-(DIHYDROXYBORANYL)ETHYL]BENZOIC ACID
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12UL1Ligand/Ion3-[(2R)-2-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}-2-(DIHYDROXYBORANYL)ETHYL]BENZOIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12UL1Ligand/Ion3-[(2R)-2-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}-2-(DIHYDROXYBORANYL)ETHYL]BENZOIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
12UL1Ligand/Ion3-[(2R)-2-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}-2-(DIHYDROXYBORANYL)ETHYL]BENZOIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
12UL1Ligand/Ion3-[(2R)-2-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}-2-(DIHYDROXYBORANYL)ETHYL]BENZOIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
12UL-1Ligand/Ion3-[(2R)-2-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}-2-(DIHYDROXYBORANYL)ETHYL]BENZOIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
12UL1Ligand/Ion3-[(2R)-2-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}-2-(DIHYDROXYBORANYL)ETHYL]BENZOIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:69 , SER A:70 , GLU A:104 , SER A:130 , ASN A:132 , GLU A:166 , ASN A:170 , LYS A:234 , SER A:235 , GLY A:236 , ALA A:237 , ARG A:244BINDING SITE FOR RESIDUE 2UL A 301
2AC2SOFTWAREGLU A:197 , MET B:69 , SER B:70 , GLU B:104 , TYR B:105 , SER B:130 , ASN B:132 , GLU B:166 , PRO B:167 , LEU B:169 , ASN B:170 , LYS B:234 , SER B:235 , GLY B:236 , ALA B:237 , GLY B:238 , ARG B:244BINDING SITE FOR RESIDUE 2UL B 301
3AC3SOFTWAREHIS B:96 , HOH B:407BINDING SITE FOR RESIDUE ZN B 302
4AC4SOFTWAREMET C:69 , SER C:70 , GLU C:104 , SER C:130 , ASN C:132 , GLU C:166 , ASN C:170 , LYS C:234 , SER C:235 , GLY C:236 , ALA C:237 , GLY C:238 , ARG C:244BINDING SITE FOR RESIDUE 2UL C 301
5AC5SOFTWAREMET D:69 , SER D:70 , GLU D:104 , TYR D:105 , SER D:130 , ASN D:132 , GLU D:166 , ASN D:170 , SER D:235 , GLY D:236 , ALA D:237 , GLU D:240 , ARG D:244BINDING SITE FOR RESIDUE 2UL D 301
6AC6SOFTWAREMET F:69 , SER F:70 , SER F:130 , ASN F:132 , GLU F:166 , ASN F:170 , VAL F:216 , LYS F:234 , SER F:235 , GLY F:236 , ALA F:237 , ARG F:244BINDING SITE FOR RESIDUE 2UL F 301

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:77 -A:123
2B:77 -B:123
3C:77 -C:123
4D:77 -D:123
5E:77 -E:123
6F:77 -F:123

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Glu A:166 -Pro A:167
2Glu B:166 -Pro B:167
3Glu C:166 -Pro C:167
4Glu D:166 -Pro D:167
5Glu E:166 -Pro E:167
6Glu F:166 -Pro F:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OQG)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh.....hhhhh....eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhh.....eeeeeeee.....eeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oqg A  26 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW 290
                                    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                                    


Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhhh......ee............hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oqg B  26 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW 290
                                    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                                    


Chain C from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee............hhhhh....eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh............hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oqg C  26 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW 290
                                    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                                    


Chain D from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee............hhhhh....eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh............hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhh.....eeeeeeeee...eeeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oqg D  26 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW 290
                                    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                                    


Chain E from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh.....hhhhh....eehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oqg E  26 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW 290
                                    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                                    


Chain F from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh.....hhhhh....eehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......hhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oqg F  26 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW 290
                                    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)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4OQG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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        Q79DR3_ECOLX | Q79DR3: 3c7u 3c7v 3dtm 3toi

(-) Related Entries Specified in the PDB File

4ibr CRYSTAL STRUCTURE OF STABILIZED TEM-1 BETA-LACTAMASE VARIANT V.13 CARRYING G238S/E104K MUTATIONS
4ibx CRYSTAL STRUCTURE OF STABILIZED TEM-1 BETA-LACTAMASE VARIANT V.13
4op5 CRYSTAL STRUCTURE OF STABILIZED TEM-1 BETA-LACTAMASE VARIANT V.13 CARRYING R164S MUTATION
4op8 ROOM TEMPERATURE CRYSTAL STRUCTURE OF STABILIZED TEM-1 BETA -LACTAMASE VARIANT V.13 CARRYING G238S MUTATION
4opq ROOM TEMPERATURE CRYSTAL STRUCTURE OF STABILIZED TEM-1 BETA -LACTAMASE VARIANT V.13 CARRYING R164S/G238S MUTATIONS
4opr CRYSTAL STRUCTURE OF STABILIZED TEM-1 BETA-LACTAMASE VARIANT V.13 CARRYING G238S MUTATION
4opy
4opz
4oq0
4oqh
4oqi