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(-) Description

Title :  CRYSTAL STRUCTURE OF THE V130D MUTANT OF OXA-24/40 IN COMPLEX WITH DORIPENEM
 
Authors :  R. A. Powers, D. A. Leonard, K. D. Schneider
Date :  19 Oct 10  (Deposition) - 19 Jan 11  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Carbapenemase, Hydrolase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. D. Schneider, C. J. Ortega, N. A. Renck, R. A. Bonomo, R. A. Powers, D. A. Leonard
Structures Of The Class D Carbapenemase Oxa-24 From Acinetobacter Baumannii In Complex With Doripenem.
J. Mol. Biol. V. 406 583 2011
PubMed-ID: 21215758  |  Reference-DOI: 10.1016/J.JMB.2010.12.042
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 32-275
    Gene: BLAOXA-33, BLA-OXA-40, BLAOXA-24, BLAOXA-40, OXA-24, OXA40
    Mutation: YES
    Organism Scientific: ACINETOBACTER BAUMANNII
    Organism Taxid: 470
    Synonym: BETA-LACTAMASE OXA-33, BETALACTAMASE OXA24, CARBAPENEM- HYDROLYZING BETA-LACTAMASE OXA-40, CARBAPENEM-HYDROLYZING OXACILLINASE, CLASS D BETA-LACTAMASE OXA-40, OXA-24 CLASS D BETA- LACTAMASE, OXA40

 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
14J62Ligand/Ion(4R,5S)-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4-METHYL-3-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
14J61Ligand/Ion(4R,5S)-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4-METHYL-3-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
14J61Ligand/Ion(4R,5S)-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4-METHYL-3-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
2SO43Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:80 , SER A:81 , LEU A:127 , SER A:128 , ASP A:130 , LEU A:168 , SER A:219 , GLY A:220 , TRP A:221 , GLY A:258 , SER A:259 , ARG A:261 , HOH A:359BINDING SITE FOR RESIDUE 4J6 A 300
2AC2SOFTWARELEU A:142 , GLU A:143 , HOH A:321BINDING SITE FOR RESIDUE SO4 A 1
3AC3SOFTWARELYS A:194 , LEU A:195 , HOH A:357BINDING SITE FOR RESIDUE SO4 A 2
4AC4SOFTWAREGLN A:178 , ASN A:181 , HOH A:329 , HOH A:348 , GLN B:178BINDING SITE FOR RESIDUE SO4 A 8
5AC5SOFTWAREALA B:80 , SER B:81 , SER B:128 , ASP B:130 , LEU B:168 , SER B:219 , GLY B:220 , TRP B:221 , GLY B:258 , SER B:259 , ARG B:261 , HOH B:341 , HOH B:355BINDING SITE FOR RESIDUE 4J6 B 300
6AC6SOFTWAREGLY B:141 , LEU B:142 , GLU B:143 , HOH B:330BINDING SITE FOR RESIDUE SO4 B 4
7AC7SOFTWARETHR B:226 , PRO B:227 , GLN B:228 , HOH B:334 , HOH B:343BINDING SITE FOR RESIDUE SO4 B 5
8AC8SOFTWAREGLN A:178 , GLN B:178 , ASN B:181 , HOH B:277 , HOH B:328BINDING SITE FOR RESIDUE SO4 B 7

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PAG)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:170 -Pro A:171
2Thr A:226 -Pro A:227
3Gly B:170 -Pro B:171
4Thr B:226 -Pro B:227

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PAG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PAG)

(-) Exons   (0, 0)

(no "Exon" information available for 3PAG)

(-) 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:245
 aligned with Q8RLA6_ACIBA | Q8RLA6 from UniProtKB/TrEMBL  Length:275

    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     
         Q8RLA6_ACIBA    31 FHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII 275
               SCOP domains d3paga_ A: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeeee..eeeeee.hhhhhhh...hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh.....hhhhhhhhhhh.eeeee..eeeeeeeeee.....eeeeeeeeee.....eeeeeeeeee.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pag A  31 MHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSADPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII 275
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     


Chain B from PDB  Type:PROTEIN  Length:245
 aligned with Q8RLA6_ACIBA | Q8RLA6 from UniProtKB/TrEMBL  Length:275

    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     
         Q8RLA6_ACIBA    31 FHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII 275
               SCOP domains d3pagb_ B: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Transpeptidase-3pagB01 B:32-270                                                                                                                                                                                                                ----- Pfam domains (1)
           Pfam domains (2) -Transpeptidase-3pagB02 B:32-270                                                                                                                                                                                                                ----- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeeee..eeeeee.hhhhhhh...hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh.....hhhhhhhhhhh.eeeee..eeeeeeeeee.....eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pag B  31 MHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSADPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII 275
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   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: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PAG)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Beta-lactamase (210)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8RLA6_ACIBA | Q8RLA6)
molecular function
    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:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q8RLA6_ACIBA | Q8RLA6: 5vfd
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        Q8RLA6_ACIBA | Q8RLA6: 2jc7 3fv7 3fyz 3fzc 3g4p 3mbz 3pae 3znt 4f94 4wm9 5tg4 5tg5 5tg6 5tg7

(-) Related Entries Specified in the PDB File

3isg THE NON-CARBAPENEMASE OXA-1 IN COMPLEX WITH THE SAME DRUG, DORIPENEM.
3pae STRUCTURE OF THE K84D MUTANT OF OXA-24/40 IN COMPLEX WITH DORIPENEM