3HVF - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   X-RAY CRYSTALLOGRAPHIC STRUCTURE OF CTX-M-9 S70G IN COMPLEX WITH HYDROLYZED BENZYLPENICILLIN

Authors :   J. Delmas, D. Leyssene, D. Dubois, E. Vazeille, F. Robin, R. Bonnet

Date :   16 Jun 09 (Deposition) - 26 May 10 (Release) - 06 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Beta-Lactamase, Blse, Ctx-M-9, B-Lactam, Penicillin, Benzylpenicillin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Delmas, D. Leyssene, D. Dubois, C. Birck, E. Vazeille, F. Robin, R. Bonnet
Structural Insights Into Substrate Recognition And Product Expulsion In Ctx-M Enzymes.
J. Mol. Biol. V. 400 108 2010
PubMed-ID: 20452359 | Reference-DOI: 10.1016/J.JMB.2010.04.062

Molecule 1 - CTX-M-9 EXTENDED-SPECTRUM BETA-LACTAMASE
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET9A
	Expression System Strain	:	BL21(DE03)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 29-291
	Gene	:	BLACTX-M-9, BLACTX-M-9A, BLACTX-M-9B
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	BETA-LACTAMASE, BETA-LACTAMASE CTX-M-9A, BETALACTAMASE CTX- M-9, CTX-M-9 BETA-LACTAMASE

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	PNK	2	Ligand/Ion	(2R,4S)-2-{(R)-CARBOXY[(PHENYLACETYL)AMINO]METHYL}-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PNK	1	Ligand/Ion	(2R,4S)-2-{(R)-CARBOXY[(PHENYLACETYL)AMINO]METHYL}-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	PNK	1	Ligand/Ion	(2R,4S)-2-{(R)-CARBOXY[(PHENYLACETYL)AMINO]METHYL}-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:69 , GLY A:70 , LYS A:73 , ASN A:104 , TYR A:105 , SER A:130 , ASN A:132 , ASN A:170 , THR A:235 , GLY A:236 , SER A:237 , GLY A:238 , ASP A:240 , HOH A:427 , HOH A:469 , HOH A:502 , HOH A:678 , HOH A:739	BINDING SITE FOR RESIDUE PNK A 301
2	AC2	SOFTWARE	CYS B:69 , GLY B:70 , LYS B:73 , ASN B:104 , TYR B:105 , SER B:130 , ASN B:132 , ASN B:170 , THR B:235 , GLY B:236 , SER B:237 , GLY B:238 , ASP B:240 , HOH B:330 , HOH B:350 , HOH B:442 , HOH B:741 , HOH B:777	BINDING SITE FOR RESIDUE PNK B 302

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

Asymmetric Unit

No.	Residues
1	Glu A:166	-	Pro A:167
2	Glu B:166	-	Pro B:167

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

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

(no "Exon" information available for 3HVF)

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:263
 aligned with Q9L5C8_ECOLX | Q9L5C8 from UniProtKB/TrEMBL  Length:291

    Alignment length:263
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288   
         Q9L5C8_ECOLX    29 QTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 291
               SCOP domains d3hvfa_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3hvfA00 A:25-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh...hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hvf A  25 QTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCGTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 290
                                    34        44        54  ||    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                           57|                                                                                                                                                                                238|         252|                                    
                                                            59                                                                                                                                                                                 240          254

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with Q9L5C8_ECOLX | Q9L5C8 from UniProtKB/TrEMBL  Length:291

    Alignment length:262
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289  
         Q9L5C8_ECOLX    30 TSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 291
               SCOP domains d3hvfb_ B: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3hvfB00 B:26-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhhh...hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hvf B  26 TSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCGTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 290
                                    35        45        55 ||     66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236 ||    247    || 258       268       278       288  
                                                          57|                                                                                                                                                                                238|         252|                                    
                                                           59                                                                                                                                                                                 240          254

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: automated matches (81)

Escherichia coli [TaxId: 562] (40)

1a	d3hvfa_	A:
1b	d3hvfb_	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	3hvfA00	A:25-290
1b	3hvfB00	B:26-290

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9L5C8_ECOLX | Q9L5C8)

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.
biological process
	GO:0030655	beta-lactam antibiotic catabolic process	The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
	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 Unit
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	Cis Peptide Bonds
		Glu A:166 - Pro A:167	[ RasMol ]
		Glu B:166 - Pro B:167	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3hvf
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3hlw	CTX-M-9 S70G IN COMPLEX WITH CEFOTAXIME
3hre	X-RAY CRYSTALLOGRAPHIC STRUCTURE OF CTX-M-9 S70G
3huo	X-RAY CRYSTALLOGRAPHIC STRUCTURE OF CTX-M-9 S70G IN COMPLEX WITH BENZYLPENICILLIN

Description

Compounds

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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