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(-) Description

Title :  STRUCTURE OF BPU1 BETA-LACTAMASE
 
Authors :  C. A. Smith, S. B. Vakulenko
Date :  24 Jul 15  (Deposition) - 18 Nov 15  (Release) - 30 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Beta-Lactamase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Toth, N. T. Antunes, N. K. Stewart, H. Frase, M. Bhattacharya, C. A. Smith, S. B. Vakulenko
Class D Beta-Lactamases Do Exist In Gram-Positive Bacteria.
Nat. Chem. Biol. V. 12 9 2016
PubMed-ID: 26551395  |  Reference-DOI: 10.1038/NCHEMBIO.1950

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BPUM_2340
    Organism Scientific: BACILLUS PUMILUS
    Organism Taxid: 1408

 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, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FLC3Ligand/IonCITRATE ANION
3KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FLC2Ligand/IonCITRATE ANION
3KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2FLC1Ligand/IonCITRATE ANION
3KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:100 , SER A:101 , TRP A:136 , SER A:149 , VAL A:151 , LYS A:239 , THR A:240 , GLY A:241 , SER A:242 , HOH A:413 , HOH A:416 , HOH A:477 , HOH A:564binding site for residue FLC A 301
2AC2SOFTWAREHIS A:168 , LYS A:171 , ALA A:172 , HIS A:285 , HOH A:408 , HOH A:514 , HOH A:550 , HOH A:750 , HOH A:769binding site for residue FLC A 302
3AC3SOFTWAREARG A:147 , VAL A:227 , GLN A:228 , HOH A:492 , HOH A:558 , LYS B:217 , HOH B:492binding site for residue EDO A 303
4AC4SOFTWARELYS A:217 , HOH A:476 , HOH A:498 , HOH A:501 , HOH A:510 , ARG B:147 , GLN B:228 , GLU B:230binding site for residue EDO A 304
5AC5SOFTWAREGLN B:100 , SER B:101 , TRP B:136 , SER B:149 , VAL B:151 , LYS B:239 , THR B:240 , GLY B:241 , SER B:242 , HOH B:419 , HOH B:459binding site for residue FLC B 301
6AC6SOFTWARELYS B:283 , TYR B:284 , HIS B:285 , HOH B:458 , HOH B:583binding site for residue PEG B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CTM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CTM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CTM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CTM)

(-) Exons   (0, 0)

(no "Exon" information available for 5CTM)

(-) 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:233
                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh....eeeeeee......eeehhhhhhh...hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeeee..eeeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ctm A  59 AIAWSVDEFFKNREGTFVIQEVKEKSPWVYNKKRAKERFAPQSTFkVANALIGLQTGAVRDEYDIKYWDGVKREIDNWNRDHTLGSGMRDSVVWYYQAMARDIGEERMNHWVKAIHYGNKDISGGIDQFWLSSTLRISPIEQVRFLKQLYEETLPFDLKNMRTVKRMMVQEEEKHATLYGKTGSGSDIGWYVGFIKHEHKTYILATNIKGTGIEAKDITYRILKKYHLMEASV 291
                                    68        78        88        98     | 108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288   
                                                                       104-KCX                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh....eeeeeee......eeehhhhhh....hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeeee..eeeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ctm B  59 AIAWSVDEFFKNREGTFVIQEVKEKSPWVYNKKRAKERFAPQSTFkVANALIGLQTGAVRDEYDIKYWDGVKREIDNWNRDHTLGSGMRDSVVWYYQAMARDIGEERMNHWVKAIHYGNKDISGGIDQFWLSSTLRISPIEQVRFLKQLYEETLPFDLKNMRTVKRMMVQEEEKHATLYGKTGSGSDIGWYVGFIKHEHKTYILATNIKGTGIEAKDITYRILKKYHLMEAS 290
                                    68        78        88        98     | 108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288  
                                                                       104-KCX
   Legend:   → Mismatch (orange background)
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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 5CTM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CTM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CTM)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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        A8FFI9_BACP2 | A8FFI9: 5ctn

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5ctn