2ZNB - JenaLib

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Title :   METALLO-BETA-LACTAMASE (CADMIUM-BOUND FORM)

Authors :   N. O. Concha, O. Herzberg

Date :   14 Oct 97 (Deposition) - 28 Jan 98 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Hydrolase, Beta-Lactamase, Metallo Beta-Lactamase, Cadmium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. O. Concha, B. A. Rasmussen, K. Bush, O. Herzberg
Crystal Structures Of The Cadmium- And Mercury-Substituted Metallo-Beta-Lactamase From Bacteroides Fragilis.
Protein Sci. V. 6 2671 1997
PubMed-ID: 9416622
(for further references see the PDB file header)

Molecule 1 - METALLO-BETA-LACTAMASE
	Cell Line	:	BL21
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	CCRA3 (WITHOUT SIGNAL SEQUENCE)
	Expression System Plasmid	:	PCLL2216
	Expression System Strain	:	BL21 LAMBDA DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CCRA3 (WITHOUT SIGNAL SEQUENCE)
	Organism Scientific	:	BACTEROIDES FRAGILIS
	Organism Taxid	:	817
	Other Details	:	CADMIUM IS BOUND IN THE ACTIVE SITE BINUCLEAR CENTER
	Strain	:	QMCN3
	Synonym	:	CLASS B 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 (2, 6)

No.	Name	Count	Type	Full Name
1	CD	4	Ligand/Ion	CADMIUM ION
2	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:99 , HIS A:101 , HIS A:162 , HOH A:250	BINDING SITE FOR RESIDUE CD A 1
2	AC2	SOFTWARE	ASP A:103 , CYS A:181 , HIS A:223 , HOH A:250 , HOH A:251	BINDING SITE FOR RESIDUE CD A 2
3	AC3	SOFTWARE	ASN A:55 , ASP A:69 , ASP A:103 , HOH A:255 , HOH A:261	BINDING SITE FOR RESIDUE NA A 3
4	AC4	SOFTWARE	HIS B:99 , HIS B:101 , HIS B:162 , HOH B:250	BINDING SITE FOR RESIDUE CD B 1
5	AC5	SOFTWARE	ASP B:103 , CYS B:181 , HIS B:223 , HOH B:250 , HOH B:251	BINDING SITE FOR RESIDUE CD B 2
6	AC6	SOFTWARE	ASN B:55 , ASP B:69 , ASP B:103 , HOH B:267 , HOH B:300	BINDING SITE FOR RESIDUE NA B 3
7	CD1	UNKNOWN	HIS A:99 , HIS A:101 , HIS A:162 , HOH A:250	THE CADMIUM IS LOCATED IN THE SAME POSITION AS THE ZINC IN THE NATIVE STRUCTURE.
8	CD2	UNKNOWN	ASP A:103 , CYS A:181 , HIS A:223 , HOH A:250 , HOH A:251	THE CADMIUM IS LOCATED IN THE SAME POSITION AS THE ZINC IN THE NATIVE STRUCTURE.
9	NA	UNKNOWN	ASN A:55 , ASP A:69 , ASP A:103 , HOH A:255 , HOH A:261	DEDUCED FROM THE COORDINATION. SODIUM WAS PRESENT IN THE CRYSTALLIZATION SOLUTION.

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

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

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

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.	BLAB_BACFG	96-115	2	A:96-115 B:96-115
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLAB_BACFG	172-184	2	A:172-184 B:172-184

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.	BLAB_BACFG	96-115	1	A:96-115 -
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLAB_BACFG	172-184	1	A:172-184 -

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.	BLAB_BACFG	96-115	1	- B:96-115
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLAB_BACFG	172-184	1	- B:172-184

(no "Exon" information available for 2ZNB)

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
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Chain A from PDB  Type:PROTEIN  Length:222
 aligned with BLAB_BACFG | P25910 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:228
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        
           BLAB_BACFG    21 SVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSK 248
               SCOP domains d2znba_ A: Zn metallo-be      ta-lactamase                                                                                                                                                                                           SCOP domains
               CATH domains 2znbA00 A:21-248 Metallo      -beta-lactamase, chain A                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) .eee...eeeee....eeeeeeee------eeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhh..eeeeee.....hhhh..hhhhhh...eeeeehhhhhhhhh.......eee..eeeeee..eeeeeee.........eeeee....----hhh................hhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhhh.. Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------eeeee-------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------BETA_LACTAMASE_B_1  --------------------------------------------------------BETA_LACTAMAS---------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2znb A  21 SVKISDDISITQLSDKVYTYVSLA------MVPSNGMIVINNHQAALLDTPINDAQTETLVNWVADSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSK 248
                                    30        40   |     -|       60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        
                                                  44     51

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with BLAB_BACFG | P25910 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:229
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238         
           BLAB_BACFG    19 QKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTS 247
               SCOP domains d2znbb_ B: Zn metallo-beta-l   actamase                                                                                                                                                                                               SCOP domains
               CATH domains 2znbB00 B:19-247 Metallo-bet   a-lactamase, chain A                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ...eeee..eeeee....eeeeeeeee.---.eeeeeeeeeee..eeeee.....hhhhhhhhhhhhh....eeeeee.....hhhh..hhhhhh...eeeeehhhhhhhhhh......eee..eeeeee..eeeeee...........eeee....----hhh................hhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author (1)
     Sec.struct. author (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------eeeee------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------BETA_LACTAMASE_B_1  --------------------------------------------------------BETA_LACTAMAS--------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2znb B  19 QKSVKISDDISITQLSDKVYTYVSLAEI---GMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVADSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTS 247
                                    28        38       | - |      58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238         
                                                      46  50

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

Bacteroides fragilis [TaxId: 817] (9)

1a	d2znba_	A:
1b	d2znbb_	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)

Bacteroides fragilis. Organism_taxid: 817. Strain: qmcn3. Cell_line: bl21. (1)

1a	2znbB00	B:19-247
1b	2znbA00	A:21-248

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (BLAB_BACFG | P25910)

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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	BLAB_BACFG \| P25910	:	1a7t 1a8t 1hlk 1kr3 1znb 2bmi 3znb 4znb

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Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (9, 9)

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