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Title :   STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-1 IN COMPLEX WITH DORIPENEM

Authors :   R. A. Powers

Date :   25 Aug 09 (Deposition) - 01 Dec 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Hydrolase, Lysine Carboxylation, Antibiotic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. D. Schneider, M. E. Karpen, R. A. Bonomo, D. A. Leonard, R. A. Powers
The 1. 4 A Crystal Structure Of The Class D Beta-Lactamase Oxa-1 Complexed With Doripenem.
Biochemistry V. 48 11840 2009
PubMed-ID: 19919101 | Reference-DOI: 10.1021/BI901690R

Molecule 1 - BETA-LACTAMASE OXA-1
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET12A
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 26-276
	Gene	:	BLA, OXA1
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PENICILLINASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	DRW	2	Ligand/Ion	(2S,3R,4S)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-3-METHYL-4-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID
2	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	DRW	1	Ligand/Ion	(2S,3R,4S)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-3-METHYL-4-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID
2	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	DRW	1	Ligand/Ion	(2S,3R,4S)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-3-METHYL-4-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID
2	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:66 , SER A:67 , KCX A:70 , MET A:99 , SER A:115 , VAL A:117 , LEU A:161 , LYS A:212 , THR A:213 , GLY A:214 , ALA A:215 , LEU A:255 , HOH A:306 , HOH A:357 , HOH A:370	BINDING SITE FOR RESIDUE DRW A 300
2	AC2	SOFTWARE	ASP B:66 , SER B:67 , KCX B:70 , GLY B:98 , MET B:99 , SER B:115 , VAL B:117 , LEU B:161 , LYS B:212 , THR B:213 , GLY B:214 , ALA B:215 , LEU B:255 , SER B:258 , HOH B:276 , HOH B:345 , HOH B:443	BINDING SITE FOR RESIDUE DRW B 300
3	AC3	SOFTWARE	ILE B:82 , GLU B:122 , HOH B:347	BINDING SITE FOR RESIDUE MPD B 400

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

(no "Cis Peptide Bond" information available for 3ISG)

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

Asymmetric 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.	BLO1_ECOLX	69-79	2	A:65-75 B:65-75

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_D	PS00337	Beta-lactamase class-D active site.	BLO1_ECOLX	69-79	1	A:65-75 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_D	PS00337	Beta-lactamase class-D active site.	BLO1_ECOLX	69-79	1	- B:65-75

(no "Exon" information available for 3ISG)

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:249
 aligned with BLO1_ECOLX | P13661 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:251
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275 
           BLO1_ECOLX    26 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 276
               SCOP domains d3isga_ A: Class D beta-lactamase                                                                                                                                                                                                                           SCOP domains
               CATH domains 3isgA00 A:18-274 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhh..eeeeeeeee.....eeeeehhhhhh....hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..........--..hhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee.....eeeeeeeeee......eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isg A  18 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFkIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGD--RNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 274
                                    27  ||    39   ||   51        61        71        81 ||     92       102       112       122       132       142      |152       162       172       182       192       202       212    || 223       233       243       253       263       273 
                                       30|        43|                      70-KCX       83|                                                             149  |                                                              217|                                                       
                                        33         46                                    85                                                                152                                                               219

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with BLO1_ECOLX | P13661 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:251
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275 
           BLO1_ECOLX    26 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 276
               SCOP domains d3isgb_ B: Class D beta-lactamase                                                                                                                                                                                                                           SCOP domains
               CATH domains 3isgB00 B:18-274 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh.eeeeeeeee.....eeeeehhhhhh....hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..........--..hhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee.....eeeeeeeeee......eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isg B  18 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFkIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGD--RNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 274
                                    27  ||    39   ||   51        61        71        81 ||     92       102       112       122       132       142      |152       162       172       182       192       202       212    || 223       233       243       253       263       273 
                                       30|        43|                      70-KCX       83|                                                             149  |                                                              217|                                                       
                                        33         46                                    85                                                                152                                                               219

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 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)

Escherichia coli, OXA-1 [TaxId: 562] (3)

1a	d3isga_	A:
1b	d3isgb_	B:

Asymmetric 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)

Escherichia coli. Organism_taxid: 562. (91)

1a	3isgA00	A:18-274
1b	3isgB00	B:18-274

(no "Pfam Domain" information available for 3ISG)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BLO1_ECOLX | P13661)

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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