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Title :   ADAPTIVE PROTEIN EVOLUTION GRANTS ORGANISMAL FITNESS BY IMPROVING CATALYSIS AND FLEXIBILITY

Authors :   P. Tomatis, S. Fabiane, F. Simona, P. Carloni, B. Sutton, A. Vila

Date :   24 Nov 08 (Deposition) - 09 Dec 08 (Release) - 13 Jan 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Metallo-Beta-Lactamase, Antibiotic Resistance, Hydrolase, Metal-Binding, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. E. Tomatis, S. M. Fabiane, F. Simona, P. Carloni, B. J. Sutton, A. J. Vila
Adaptive Protein Evolution Grants Organismal Fitness By Improving Catalysis And Flexibility.
Proc. Natl. Acad. Sci. Usa V. 105 20605 2008
PubMed-ID: 19098096 | Reference-DOI: 10.1073/PNAS.0807989106
(for further references see the PDB file header)

Molecule 1 - BETA-LACTAMASE 2
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	BLM
	Mutation	:	YES
	Organism Scientific	:	BACILLUS CEREUS
	Organism Taxid	:	1396
	Strain	:	569/H/9
	Synonym	:	BETA-LACTAMASE II, PENICILLINASE, CEPHALOSPORINASE

		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, 4)

No.	Name	Count	Type	Full Name
1	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:116 , HIS A:118 , ASP A:120 , HIS A:196 , ZN A:293	BINDING SITE FOR RESIDUE ZN A 292
2	AC2	SOFTWARE	ASP A:120 , CYS A:221 , HIS A:263 , ZN A:292	BINDING SITE FOR RESIDUE ZN A 293
3	AC3	SOFTWARE	HIS B:116 , HIS B:118 , ASP B:120 , HIS B:196 , ZN B:293	BINDING SITE FOR RESIDUE ZN B 292
4	AC4	SOFTWARE	HOH B:11 , ASP B:120 , CYS B:221 , HIS B:263 , ZN B:292 , HOH B:299	BINDING SITE FOR RESIDUE ZN B 293

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

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_B_1	PS00743	Beta-lactamases class B signature 1.	BLA2_BACCE	113-132	2	A:113-133 B:113-133
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLA2_BACCE	189-201	2	A:209-224 B:209-224

Biological Unit 1 (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.	BLA2_BACCE	113-132	1	A:113-133 -
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLA2_BACCE	189-201	1	A:209-224 -

Biological Unit 2 (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.	BLA2_BACCE	113-132	1	- B:113-133
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLA2_BACCE	189-201	1	- B:209-224

(no "Exon" information available for 3FCZ)

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:219
 aligned with BLA2_BACCE | P04190 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:222
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255  
           BLA2_BACCE    36 KTVIKNETGTISISQLNKNVWVHTELGSFNGEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADRIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVPGHGEVGDKGLLLHTLDLLK 257
               SCOP domains d3fcza_ A: Zn metallo-beta-la   ctamase                                                                                                                                                                                        SCOP domains
               CATH domains 3fczA00 A:32-291 Metallo-beta   -lactamase, chain A                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee......eeee....eeeeeee...---..eeeeeeeee..eeeee....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..eee.hhhhhhhhhhh...........eeeeee..eeeeee...........eeee....eeeeehhh................hhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------BETA_LACTAMASE_B_1  --------------------------------------------------------BETA_LACTAMAS-------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fcz A  32 KTVIKNETGTISISQLNKNVWVHTELGSF---AVPSSGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDAIITHAHADRIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVSKRYRNINAVVPSHGEVGDKGLLLHTLDLLK 291
                                    41   ||   52        |-  |     73        83        93      |104  ||   115       125     ||136       146   ||  172       182       192       202  || ||218       228       238       248       258      |279       289  
                                        45|            61  66                               100|  107|                   131|              150|                                   205| ||                                               265|              
                                         47                                                  102   109                    133               167                                    209 ||                                                277              
                                                                                                                                                                                     211|                                                                 
                                                                                                                                                                                      215

Chain B from PDB  Type:PROTEIN  Length:219
 aligned with BLA2_BACCE | P04190 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:222
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255  
           BLA2_BACCE    36 KTVIKNETGTISISQLNKNVWVHTELGSFNGEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADRIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVPGHGEVGDKGLLLHTLDLLK 257
               SCOP domains d3fczb_ B: Zn metallo-beta-la   ctamase                                                                                                                                                                                        SCOP domains
               CATH domains 3fczB00 B:32-291 Metallo-beta   -lactamase, chain A                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee......eeee....eeeeeee...---..eeeeeeeee..eeeee....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..eee.hhhhhhhhhhh...........eeeeee..eeeeee...........eeee....eeeeehhh................hhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------BETA_LACTAMASE_B_1  --------------------------------------------------------BETA_LACTAMAS-------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fcz B  32 KTVIKNETGTISISQLNKNVWVHTELGSF---AVPSSGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDAIITHAHADRIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVSKRYRNINAVVPSHGEVGDKGLLLHTLDLLK 291
                                    41   ||   52        |-  |     73        83        93      |104  ||   115       125     ||136       146   ||  172       182       192       202  || ||218       228       238       248       258      |279       289  
                                        45|            61  66                               100|  107|                   131|              150|                                   205| ||                                               265|              
                                         47                                                  102   109                    133               167                                    209 ||                                                277              
                                                                                                                                                                                     211|                                                                 
                                                                                                                                                                                      215

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: 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)

Bacillus cereus [TaxId: 1396] (16)

1a	d3fcza_	A:
1b	d3fczb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Metallo-beta-lactamase; Chain A (92)

Homologous Superfamily: Metallo-beta-lactamase, chain A (92)

Bacillus cereus. Organism_taxid: 1396. Strain: 569/h/9. (1)

1a	3fczA00	A:32-291
1b	3fczB00	B:32-291

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (BLA2_BACCE | P04190)

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).

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Description

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