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Title :   CRYSTAL STRUCTURE OF THE ACYL-ENZYME OXA-10 W154A-BENZYLPENICILLIN AT PH 6

Authors :   L. Vercheval, C. Falzone, E. Sauvage, R. Herman, P. Charlier, M. Gallen F. Kerff

Date :   20 Apr 09 (Deposition) - 10 Nov 09 (Release) - 23 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

Chains :   Asym./Biol. Unit : A,B

Keywords :   Hydrolase-Antibiotic Complex, Hydrolase Antibiotic Complex, Lysine Carboxylation, Hydrolase, Acyl-Enzyme, Antibiotic Resistance, Class D Beta-Lactamase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Baurin, L. Vercheval, F. Bouillenne, C. Falzone, A. Brans, L. Jacquamet, J. L. Ferrer, E. Sauvage, D. Dehareng, J. M. Frere, P. Charlier, M. Galleni, F. Kerff
Critical Role Of Tryptophan 154 For The Activity And Stability Of Class D Beta-Lactamases.
Biochemistry V. 48 11252 2009
PubMed-ID: 19860471 | Reference-DOI: 10.1021/BI901548C

Molecule 1 - BETA-LACTAMASE OXA-10
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET 22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Synonym	:	BETA-LACTAMASE PSE-2

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	PNM	2	Ligand/Ion	OPEN FORM - PENICILLIN G

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:66 , SER A:67 , SER A:115 , VAL A:117 , LEU A:155 , THR A:206 , PHE A:208 , ARG A:250	BINDING SITE FOR RESIDUE PNM A 700
2	AC2	SOFTWARE	ALA B:66 , SER B:67 , SER B:115 , VAL B:117 , LEU B:155 , THR B:206 , PHE B:208 , ARG B:250	BINDING SITE FOR RESIDUE PNM B 700

Asymmetric/Biological Unit

No.	Residues
1	A:44	-	A:51
2	B:44	-	B:51

(no "Cis Peptide Bond" information available for 2WGI)

(no "SAP(SNP)/Variant" information available for 2WGI)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_D	PS00337	Beta-lactamase class-D active site.	BLO10_PSEAI	65-75	2	A:65-75 B:65-75

(no "Exon" information available for 2WGI)

Asymmetric/Biological 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:234
 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 d2wgia_ A: Class D beta-lactamase                                                                                                                                                                                                                    SCOP domains
               CATH domains 2wgiA00 A:21-264 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhh...eeeeeee.....eee.hhhhhh....hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...----------........hhhhhhhhhhhhhhh....hhhhhhhhhhhheeee...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------BETA_LACTAM--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wgi A  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGN----------ALEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
                                    30        40        50        60        70        80        90       100       110       120       130       140  |      -   |   160       170       180       190       200       210       220       230       240       250       260    
                                                                                                                                                    143        154

Chain B from PDB  Type:PROTEIN  Length:247
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:247
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       
          BLO10_PSEAI    19 AGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
               SCOP domains d2wgib_ B: Class D beta-lactamase                                                                                                                                                                                                                       SCOP domains
               CATH domains 2wgiB00 B:19-265 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhh...eeeeeee....eeee.hhhhhhhee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh...eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------BETA_LACTAM---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wgi B  19 MGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFALEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: beta-lactamase/transpeptidase-like (515)

Superfamily: beta-lactamase/transpeptidase-like (515)

Family: beta-Lactamase/D-ala carboxypeptidase (411)

Protein domain: Class D beta-lactamase (32)

Pseudomonas aeruginosa, OXA-10 [TaxId: 287] (25)

1a	d2wgia_	A:
1b	d2wgib_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Beta-lactamase (339)

Homologous Superfamily: DD-peptidase/beta-lactamase superfamily (335)

Pseudomonas aeruginosa. Organism_taxid: 287. (17)

1a	2wgiB00	B:19-265
1b	2wgiA00	A:21-264

(no "Pfam Domain" information available for 2WGI)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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1e3u	MAD STRUCTURE OF OXA10 CLASS D BETA- LACTAMASE
1e4d	STRUCTURE OF OXA10 BETA-LACTAMASE AT PH 8.3
1ewz	CRYSTAL STRUCTURE OF THE OXA-10 BETA- LACTAMASE FROM PSEUDOMONAS AERUGINOSA
1fof	CRYSTAL STRUCTURE OF THE CLASS D BETA- LACTAMASE OXA-10
1k4e	CRYSTAL STRUCTURE OF THE CLASS D BETA- LACTAMASES OXA-10DETERMINED BY MAD PHASING WITH SELENOMETHIONINE
1k4f	CRYSTAL STRUCTURE OF THE CLASS D BETA- LACTAMASE OXA-10 AT1.6 A RESOLUTION
1k54	OXA-10 CLASS D BETA-LACTAMASE PARTIALLY ACYLATED WITHREACTED 6BETA-(1-HYDROXY-1- METHYLETHYL) PENICILLANIC ACID
1k55	OXA 10 CLASS D BETA-LACTAMASE AT PH 7.5
1k56	OXA 10 CLASS D BETA-LACTAMASE AT PH 6.5
1k57	OXA 10 CLASS D BETA-LACTAMASE AT PH 6.0
1k6r	STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-10 IN COMPLEXWITH MOXALACTAM
1k6s	STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-10 IN COMPLEXWITH A PHENYLBORONIC ACID

Description

Compounds

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Ligands, Modified Residues, Ions (2, 3)

Sites (2, 2)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

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Gene Ontology (5, 5)

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