3ZNB - JenaLib

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Title :   METALLO-BETA-LACTAMASE (ZN, HG-BOUND FORM)

Authors :   N. O. Concha, O. Herzberg

Date :   15 Oct 97 (Deposition) - 28 Jan 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Hydrolase, Beta-Lactamase, Metallo Beta-Lactamase, Mercury, Zinc (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
	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	:	ONE ZINC AND ONE MERCURY ARE BOUND IN THE ACTIVE SITE
	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 (3, 6)

No.	Name	Count	Type	Full Name
1	HG	2	Ligand/Ion	MERCURY (II) ION
2	NA	2	Ligand/Ion	SODIUM ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	HG	-1	Ligand/Ion	MERCURY (II) ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	HG	-1	Ligand/Ion	MERCURY (II) ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:99 , HIS A:101 , HIS A:162	BINDING SITE FOR RESIDUE ZN A 1
2	AC2	SOFTWARE	ASP A:69 , HIS A:99 , ASP A:103 , CYS A:104 , CYS A:181 , HOH A:262	BINDING SITE FOR RESIDUE HG A 2
3	AC3	SOFTWARE	TYR A:40 , ASN A:55 , ASP A:69 , THR A:70 , ASP A:103 , HOH A:258	BINDING SITE FOR RESIDUE NA A 3
4	AC4	SOFTWARE	HIS B:99 , HIS B:101 , HIS B:162	BINDING SITE FOR RESIDUE ZN B 1
5	AC5	SOFTWARE	ASP B:69 , HIS B:99 , ASP B:103 , CYS B:104 , CYS B:181 , HOH B:259	BINDING SITE FOR RESIDUE HG B 2
6	AC6	SOFTWARE	ASN B:55 , ASP B:69 , ASP B:103 , HOH B:259	BINDING SITE FOR RESIDUE NA B 3
7	HG	UNKNOWN	CYS A:104 , CYS A:181	ZN2 WAS EJECTED AND THE MERCURY IS BOUND IN A DIFFERENT POSITION.
8	NA	UNKNOWN	ASP A:69 , ASN A:55 , ASP A:103	DEDUCED FROM THE COORDINATION IN THE NATIVE STRUCTURE. SODIUM WAS PRESENT IN THE CRYSTALLIZATION SOLUTION.
9	ZN	UNKNOWN	HIS A:99 , HIS A:101 , HIS A:162	THE ZINC IS LOCATED IN THE SAME POSITION AS ZN1 IN THE NATIVE STRUCTURE.

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

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

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

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 3ZNB)

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:226
 aligned with BLAB_BACFG | P25910 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:229
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239         
           BLAB_BACFG    20 KSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSK 248
               SCOP domains d3znba_ A: Zn metallo-beta-l  actamase                                                                                                                                                                                                SCOP domains
               CATH domains 3znbA00 A:20-248 Metallo-bet  a-lactamase, chain A                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eee...eeeee....eeeeeeeee..--.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
                 3znb A  20 KSVKISDDISITQLSDKVYTYVSLAEIE--GMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVADSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIEST-K 248
                                    29        39       | -|       59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239      | |
                                                      47 50                                                                                                                                                                                                 246 |
                                                                                                                                                                                                                                                              248

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with BLAB_BACFG | P25910 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:229
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239         
           BLAB_BACFG    20 KSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSK 248
               SCOP domains d3znbb_ B: Zn metallo-beta-l  actamase                                                                                                                                                                                                SCOP domains
               CATH domains 3znbB00 B:20-248 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
                 3znb B  20 KSVKISDDISITQLSDKVYTYVSLAEIE--GMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVADSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSK 248
                                    29        39       | -|       59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239         
                                                      47 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(

)

Folds(

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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)

Bacteroides fragilis [TaxId: 817] (9)

1a	d3znba_	A:
1b	d3znbb_	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. (1)

1a	3znbB00	B:20-248
1b	3znbA00	A:20-248

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

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).

Asymmetric Unit
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	Cis Peptide Bonds
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	3znb
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	BLAB_BACFG \| P25910	:	1a7t 1a8t 1hlk 1kr3 1znb 2bmi 2znb 4znb

(no "Related Entries Specified in the PDB File" available for 3ZNB)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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