2X02 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-10 AT 1.35 A RESOLUTION

Authors :   L. Vercheval, F. Kerff, E. Sauvage, R. Herman, M. Galleni, P. Charlier

Date :   04 Dec 09 (Deposition) - 08 Dec 10 (Release) - 08 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

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

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

Reference :   L. Vercheval, F. Kerff, C. Bauvois, E. Sauvage, R. Guiet, F. Borel, J. L. Ferrer, P. Charlier, M. Galleni
Impact Of The Carboxylated Lysine On The Acylation And Deacylation Step In Class D Beta-Lactamase
To Be Published
PubMed: search

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
	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 (5, 10)

No.	Name	Count	Type	Full Name
1	DMS	4	Ligand/Ion	DIMETHYL SULFOXIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL
5	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:67 , SER A:115 , LYS A:205 , THR A:206 , GLY A:207 , PHE A:208 , ARG A:250 , HOH A:2060 , HOH A:2319 , HOH A:2320 , HOH A:2321	BINDING SITE FOR RESIDUE SO4 A1266
2	AC2	SOFTWARE	SER A:215 , ASN A:216 , HOH A:2288 , HOH A:2322 , HOH A:2324 , GLN B:158 , ARG B:160 , HOH B:2137	BINDING SITE FOR RESIDUE PG4 A1267
3	AC3	SOFTWARE	HIS A:87 , VAL A:89 , TYR B:174 , LEU B:175	BINDING SITE FOR RESIDUE PG4 B1266
4	AC4	SOFTWARE	TYR B:63 , LEU B:64 , SER B:209 , VAL B:219	BINDING SITE FOR RESIDUE DMS B1267
5	AC5	SOFTWARE	HOH A:2324 , GLU B:62 , GLY B:142 , HOH B:2154	BINDING SITE FOR RESIDUE DMS A1270
6	AC6	SOFTWARE	TYR A:63 , LEU A:64 , PRO A:217 , HOH A:2053	BINDING SITE FOR RESIDUE DMS A1268
7	AC7	SOFTWARE	ASN A:29 , PHE A:32 , VAL A:37 , ASN A:38 , GLY A:39 , ASN A:54 , ASP A:55	BINDING SITE FOR RESIDUE DMS A1269
8	AC8	SOFTWARE	ASN B:29 , PHE B:32 , VAL B:37 , ASN B:38 , GLY B:39 , ASN B:54 , ASP B:55	BINDING SITE FOR RESIDUE GOL B1268

Asymmetric/Biological Unit

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

(no "Cis Peptide Bond" information available for 2X02)

(no "SAP(SNP)/Variant" information available for 2X02)

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 2X02)

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:245
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:245
                                    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 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
               SCOP domains d2x02a_ A: Class D beta-lactamase                                                                                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhh....eeeeeee.....eee.hhhhhh.ee.hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh...eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------BETA_LACTAM---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x02 A  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
                                    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 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 d2x02b_ B: Class D beta-lactamase                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhh...eeeeeee....eeee.hhhhhhhee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------BETA_LACTAM---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x02 B  19 MGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 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       
                                                                              70-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 '\|'

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	d2x02a_	A:
1b	d2x02b_	B:

(no "CATH Domain" information available for 2X02)

(no "Pfam Domain" information available for 2X02)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2x02)

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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
2wgi	CRYSTAL STRUCTURE OF THE ACYL-ENZYME OXA- 10 W154A-BENZYLPENICILLIN AT PH 6
2wgv	CRYSTAL STRUCTURE OF THE OXA-10 V117T MUTANT AT PH 6.5 INHIBITED BY A CHLORIDE ION
2wgw	CRYSTAL STRUCTURE OF THE OXA-10 V117T MUTANT AT PH 8.0
2wkh	CRYSTAL STRUCTURE OF THE ACYL-ENZYME OXA- 10 K70C-AMPICILLIN AT PH 7
2wki	CRYSTAL STRUCTURE OF THE OXA-10 K70C MUTANT AT PH 7.0
2x01	CRYSTAL STRUCTURE OF THE OXA-10 S67A MUTANT AT PH 7

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (8, 8)

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 (0, 0)

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Gene Ontology (5, 5)

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