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(-) Description

Title :  CRYSTAL STRUCTURE OF 6ALPHA-HYDROXYMETHYLPENICILLANATE COMPLEXED WITH OXA-58, A CARBAPENEM HYDROLYZING CLASS D BETALACTAMASE FROM ACINETOBACTER BAUMANII.
 
Authors :  S. Pratap, M. Katiki, P. Gill, D. Golemi-Kotra, P. Kumar
Date :  06 Feb 15  (Deposition) - 13 Jan 16  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
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 :  Acyl-Enzyme Complex, Oxa-58, 6Alpha-Hydroxymethylpenicillanate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Pratap, M. Katiki, P. Gill, P. Kumar, D. Golemi-Kotra
Active-Site Plasticity Is Essential To Carbapenem Hydrolysi By Oxa-58 Class D Beta-Lactamase Of Acinetobacter Baumannii
Antimicrob. Agents Chemother. V. 60 75 2015
PubMed-ID: 26459904  |  Reference-DOI: 10.1128/AAC.01393-15

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B, C, D
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: BLA-OXA-58, BLA-OXA58
    Organism Scientific: ACINETOBACTER BAUMANNII
    Organism Taxid: 470

 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1ALP4Ligand/Ion2-(1-CARBOXY-2-HYDROXY-ETHYL)-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID
2KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ALP1Ligand/Ion2-(1-CARBOXY-2-HYDROXY-ETHYL)-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ALP1Ligand/Ion2-(1-CARBOXY-2-HYDROXY-ETHYL)-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1ALP1Ligand/Ion2-(1-CARBOXY-2-HYDROXY-ETHYL)-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1ALP1Ligand/Ion2-(1-CARBOXY-2-HYDROXY-ETHYL)-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:82 , SER A:83 , KCX A:86 , SER A:130 , VAL A:132 , SER A:221 , GLY A:222 , TRP A:223 , MET A:225 , ARG A:263binding site for residue ALP A 301
2AC2SOFTWAREPRO B:81 , ALA B:82 , THR B:84 , PHE B:85 , KCX B:86 , SER B:130 , VAL B:132 , LEU B:170 , LYS B:220 , SER B:221 , GLY B:222 , TRP B:223 , ARG B:263binding site for Di-peptide ALP B 301 and SER B 83
3AC3SOFTWAREPRO C:81 , ALA C:82 , THR C:84 , PHE C:85 , KCX C:86 , SER C:130 , VAL C:132 , LYS C:220 , SER C:221 , GLY C:222 , TRP C:223 , ARG C:263 , HOH C:416binding site for Di-peptide ALP C 301 and SER C 83
4AC4SOFTWAREPRO D:81 , ALA D:82 , THR D:84 , PHE D:85 , KCX D:86 , SER D:130 , VAL D:132 , LYS D:220 , SER D:221 , GLY D:222 , TRP D:223 , MET D:225 , ARG D:263binding site for Di-peptide ALP D 301 and SER D 83

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y0U)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:172 -Pro A:173
2Asp A:228 -Pro A:229
3Gly B:172 -Pro B:173
4Asp B:228 -Pro B:229
5Gly C:172 -Pro C:173
6Asp C:228 -Pro C:229
7Gly D:172 -Pro D:173
8Asp D:228 -Pro D:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y0U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y0U)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y0U)

(-) 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:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh......eeeeee....eeee..hhhhhhh...hhhhhhhhhhhhhhhh.......ee........hhhhh..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhheeeee..eeeeeeeeee.....eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y0u A  38 SIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFkIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHYL 280
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277   
                                                                           86-KCX                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh......eeeeee....eeee..hhhhhhh...hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhheeeee..eeeeeeeeee.....eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y0u B  38 SIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFkIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHYL 280
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277   
                                                                           86-KCX                                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh......eeeeee....eeee..hhhhhhh...hhhhhhhhhhhhhhhh.......ee........hhhhh..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhheeeee..eeeeeeeeee.....eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y0u C  39 IIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFkIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHYL 280
                                    48        58        68        78       |88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278  
                                                                          86-KCX                                                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......eeeeee....eeee..hhhhhhh...hhhhhhhhhhhhhhhh.......ee........hhhhh..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhheeeee..eeeeeeeeee.....eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y0u D  37 NSIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFkIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHY 279
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276   
                                                                            86-KCX
   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 4Y0U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y0U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y0U)

(-) Gene Ontology  (5, 5)

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 Related Entries

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        Q2TR58_ACIBA | Q2TR58: 4oh0 4y0o 4y0t 5boh

(-) Related Entries Specified in the PDB File

4y0o 4y0t