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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE ZINC CARBAPENEMASE CPHA IN COMPLEX WITH THE INHIBITOR PYRIDINE-2,4-DICARBOXYLATE

Authors :   G. Garau, O. Dideberg

Date :   03 Apr 06 (Deposition) - 13 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.86

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Lactamase, Inhibitor, Zn (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. E. Horsfall, G. Garau, B. M. R. Lienard, O. Dideberg, C. J. Schofield J. M. Frere, M. Galleni
Competitive Inhibitors Of The Cpha Metallo-{Beta}-Lactamase From Aeromonas Hydrophila
Antimicrob. Agents Chemother. V. 51 2136 2007
PubMed-ID: 17307979 | Reference-DOI: 10.1128/AAC.00866-06
(for further references see the PDB file header)

Molecule 1 - BETA-LACTAMASE
	Chains	:	A
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC20-CPHA
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CPHA
	Organism Scientific	:	AEROMONAS HYDROPHILA
	Organism Taxid	:	644

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	PD2	1	Ligand/Ion	PYRIDINE-2,4-DICARBOXYLIC ACID
3	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PD2 A:2 , ASP A:120 , CYS A:221 , HIS A:263	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	VAL A:67 , ASP A:120 , HIS A:196 , CYS A:221 , LYS A:224 , GLY A:232 , ASN A:233 , HIS A:263 , ZN A:401 , HOH A:402 , HOH A:407 , HOH A:531	BINDING SITE FOR RESIDUE PD2 A 2
3	AC3	SOFTWARE	ARG A:188 , PHE A:190 , TYR A:204 , MET A:252 , LEU A:254 , HOH A:491	BINDING SITE FOR RESIDUE GOL A 3
4	AC4	SOFTWARE	HIS A:176 , ASP A:177 , GLY A:178 , ASP A:179	BINDING SITE FOR RESIDUE GOL A 4
5	AC5	SOFTWARE	LEU A:267 , HIS A:289 , GLY A:290 , GLU A:292 , HOH A:515 , HOH A:568	BINDING SITE FOR RESIDUE GOL A 5

(no "SS Bond" information available for 2GKL)

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

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_B_1	PS00743	Beta-lactamases class B signature 1.	BLAB_AERHY	92-111	1	A:113-133
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLAB_AERHY	184-196	1	A:209-224

(no "Exon" information available for 2GKL)

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:225
 aligned with BLAB_AERHY | P26918 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:225
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247     
           BLAB_AERHY    28 AGMSLTQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRKPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKTVIGGHDSPLHGPELIDHYEALIKAAP 252
               SCOP domains d2gkla_ A: Zn metallo-beta-lactamase                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeee.....eeeeeee....eeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhhh............eee...eee....eeee...........eeee....eee.hhhh............hhhhhhhhhhhhh.....eee......ee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------BETA_LACTAMASE_B_1  ------------------------------------------------------------------------BETA_LACTAMAS-------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gkl A  41 AGMSLTQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRKPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKTVIGGHDSPLHGPELIDHYEALIKAAP 305
                                    50        60|       76        86        96   ||  108       118       128  ||   139       149       159       169       179       189       199     ||215       225||     239       249       259       290       300     
                                              60|                              100| 106|                    131|                                                                     205| ||        226|                                 267|                
                                               67                               102  108                     133                                                                      209 ||         231                                  289                
                                                                                                                                                                                        211|                                                                 
                                                                                                                                                                                         215

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Metallo-hydrolase/oxidoreductase (184)

Superfamily: Metallo-hydrolase/oxidoreductase (184)

Family: Zn metallo-beta-lactamase (93)

Protein domain: Zn metallo-beta-lactamase (63)

Aeromonas hydrophila, CphA [TaxId: 644] (11)

d2gkla_

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (BLAB_AERHY | P26918)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2gkl)

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	2gkl
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	3.5.2.6
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	BLAB_AERHY \| P26918	:	1x8g 1x8h 1x8i 2qds 3f9o 3fai 3iof 3iog 3sw3 3t9m

1x8g	THE MONO-ZINC CARBAPENEMASE
1x8h	THE MONO-ZINC CARBAPENEMASE CPHA (N220G MUTANT) SHOWS A ZN(II)- NH2 ARG COORDINATION
1x8i	THE SAME PROTEIN WITH THE ANTIBIOTIC BIAPENEM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SCOP Domains (1, 1)

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Gene Ontology (7, 7)

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