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(-) Description

Title :  STRUCTURE OF OXA10 BETA-LACTAMASE AT PH 8.3
 
Authors :  L. Maveyraud, D. Golemi, L. P. Kotra, S. Tranier, S. Vakulenko, S. Mobashery, J. P. Samama
Date :  03 Jul 00  (Deposition) - 12 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Beta-Lactamase, Antiobitic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Maveyraud, D. Golemi, L. P. Kotra, S. Tranier, S. Vakulenko, S. Mobashery, J. P. Samama
Insights Into Class D Beta-Lactamases Are Revealed By The Crystal Structure Of The Oxa10 Enzyme From Pseudomonas Aeruginosa
Structure V. 8 1289 2000
PubMed-ID: 11188693  |  Reference-DOI: 10.1016/S0969-2126(00)00534-7

(-) Compounds

Molecule 1 - BETA-LACTAMASE OXA-10
    ChainsA, B, C, D
    EC Number3.5.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationEXCRETED
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePET24A
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid287

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 26)

Asymmetric Unit (3, 26)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO416Ligand/IonSULFATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO48Ligand/IonSULFATE ION
Biological Unit 2 (3, 14)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO48Ligand/IonSULFATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:67 , SER A:115 , LYS A:205 , THR A:206 , GLY A:207 , PHE A:208 , ARG A:250 , HOH A:2177 , HOH A:2219 , HOH A:2220 , HOH A:2221BINDING SITE FOR RESIDUE SO4 A 901
02AC2SOFTWARETHR A:80 , ARG A:131 , LYS A:134 , TYR A:135BINDING SITE FOR RESIDUE SO4 A 902
03AC3SOFTWAREMET A:99 , LYS A:100 , GLN A:101BINDING SITE FOR RESIDUE SO4 A 903
04AC4SOFTWAREGLY A:128 , GLU A:129 , VAL A:130 , HOH A:2222 , HOH A:2224 , HOH A:2225BINDING SITE FOR RESIDUE SO4 A 904
05AC5SOFTWAREASN B:85 , HOH B:2243 , HOH B:2244 , ASN D:176 , LYS D:182 , HOH D:2171BINDING SITE FOR RESIDUE SO4 B 901
06AC6SOFTWAREPRO B:198 , GLU B:199 , GLU B:227 , GLU B:229 , HOH B:2245 , HOH B:2246 , THR D:107 , ARG D:109BINDING SITE FOR RESIDUE SO4 B 902
07AC7SOFTWARESER B:67 , SER B:115 , LYS B:205 , THR B:206 , GLY B:207 , PHE B:208 , ARG B:250 , HOH B:2198 , HOH B:2247BINDING SITE FOR RESIDUE SO4 B 903
08AC8SOFTWAREARG B:160BINDING SITE FOR RESIDUE SO4 B 904
09AC9SOFTWARETHR B:80 , ARG B:131 , LYS B:134 , TYR B:135BINDING SITE FOR RESIDUE SO4 B 905
10BC1SOFTWAREGLU C:195 , TYR C:200 , VAL C:202 , TRP C:222 , VAL C:226 , THR C:255 , MET C:258 , HOH C:2164 , HOH C:2214BINDING SITE FOR RESIDUE SO4 C 901
11BC2SOFTWARETHR C:206 , LEU C:247 , PRO C:248 , ARG C:250 , LYS C:251 , HOH C:2215BINDING SITE FOR RESIDUE SO4 C 902
12BC3SOFTWAREHOH B:2101 , HOH B:2105 , MET C:99 , LYS C:100 , GLN C:101 , HOH C:2216BINDING SITE FOR RESIDUE SO4 C 903
13BC4SOFTWARESER C:67 , SER C:115 , LYS C:205 , THR C:206 , GLY C:207 , PHE C:208 , ARG C:250 , HOH C:2092 , HOH C:2217 , HOH C:2218BINDING SITE FOR RESIDUE SO4 C 904
14BC5SOFTWARELYS A:95 , SER D:67 , SER D:115 , LYS D:205 , THR D:206 , GLY D:207 , PHE D:208 , ARG D:250 , HOH D:2246BINDING SITE FOR RESIDUE SO4 D 901
15BC6SOFTWARETHR D:206 , LEU D:247 , PRO D:248 , ARG D:250 , LYS D:251BINDING SITE FOR RESIDUE SO4 D 902
16BC7SOFTWAREGLU B:183 , SER D:181 , LYS D:182 , HOH D:2247 , HOH D:2248BINDING SITE FOR RESIDUE SO4 D 903
17BC8SOFTWAREGLU A:195 , TYR A:200 , VAL A:202 , MET A:258 , GLU A:259 , ILE A:263 , HOH A:2217BINDING SITE FOR RESIDUE EDO A 911
18BC9SOFTWAREGLU B:195 , TYR B:200 , GLU B:259 , ILE B:263 , HOH B:2185 , HOH B:2249BINDING SITE FOR RESIDUE EDO B 911
19CC1SOFTWAREASN B:38 , PRO B:217 , ASP B:240 , HOH B:2027 , HOH B:2222 , HOH B:2250BINDING SITE FOR RESIDUE EDO B 912
20CC2SOFTWARETHR A:107 , ARG A:109 , PRO C:198 , GLU C:199 , TYR C:200 , GLU C:229 , HOH C:2219BINDING SITE FOR RESIDUE EDO C 911
21CC3SOFTWAREGLN D:113 , SER D:204 , LYS D:205 , THR D:206 , HOH D:2198 , HOH D:2249BINDING SITE FOR RESIDUE EDO D 911
22CC4SOFTWAREGLU D:195 , THR D:255 , HOH D:2196BINDING SITE FOR RESIDUE EDO D 912

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:44 -A:51
2B:44 -B:51
3C:44 -C:51
4D:44 -D:51

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E4D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E4D)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_DPS00337 Beta-lactamase class-D active site.BLO10_PSEAI65-75
 
 
 
  4A:65-75
B:65-75
C:65-75
D:65-75
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_DPS00337 Beta-lactamase class-D active site.BLO10_PSEAI65-75
 
 
 
  2A:65-75
-
C:65-75
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_DPS00337 Beta-lactamase class-D active site.BLO10_PSEAI65-75
 
 
 
  2-
B:65-75
-
D:65-75

(-) Exons   (0, 0)

(no "Exon" information available for 1E4D)

(-) 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
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:243
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   
          BLO10_PSEAI    22 ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
               SCOP domains d1e4da_ A: Class D beta-lactamase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1e4dA00 A:22-264 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh....eeeeeee.....eee.hhhhhh....hhhhh.hhhhhhhhhhh.................hhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------BETA_LACTAM--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e4d A  22 ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   
                                                                           70-KCX                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:244
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:244
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
          BLO10_PSEAI    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
               SCOP domains d1e4db_ B: Class D beta-lactamase                                                                                                                                                                                                                    SCOP domains
               CATH domains 1e4dB00 B:21-264 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh....eeeeeee.....eee.hhhhhh....hhhhh.hhhhhhhhhh..................hhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh.....hhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------BETA_LACTAM--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e4d B  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
                                                                            70-KCX                                                                                                                                                                                              

Chain C from PDB  Type:PROTEIN  Length:246
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:246
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
          BLO10_PSEAI    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG 266
               SCOP domains d1e4dc_ C: Class D beta-lactamase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1e4dC00 C:21-266 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.hhhhhhhhhh...eeeeeee.....eee.hhhhhhh...hhhhh.hhhhhhhhhh..................hhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1e4d C  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG 266
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
                                                                            70-KCX                                                                                                                                                                                                

Chain D from PDB  Type:PROTEIN  Length:246
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:246
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
          BLO10_PSEAI    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG 266
               SCOP domains d1e4dd_ D: Class D beta-lactamase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1e4dD00 D:21-266 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhh..eeeeeee.....eee.hhhhhhh...hhhhh.hhhhhhhhhh..................hhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh.....hhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1e4d D  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG 266
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
                                                                            70-KCX                                                                                                                                                                                                

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E4D)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (BLO10_PSEAI | P14489)
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:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BLO10_PSEAI | P144891e3u 1ewz 1fof 1k4e 1k4f 1k54 1k55 1k56 1k57 1k6r 1k6s 2hp5 2hp6 2hp9 2hpb 2rl3 2wgi 2wgv 2wgw 2wkh 2wki 2x01 2x02 3lce 4s2o 4wz5 5fq9 5mmy 5mnu 5mox 5moz

(-) Related Entries Specified in the PDB File

1e3u MAD STRUCTURE OF OXA10 CLASS D BETA-LACTAMASE