4C1G - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE IMP-1 WITH D-CAPTOPRIL

Authors :   D. Zollman, J. Brem, M. A. Mcdonough, S. S. Vanberkel, C. J. Schofield

Date :   12 Aug 13 (Deposition) - 27 Aug 14 (Release) - 13 Jan 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.71

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

Keywords :   Hydrolase, Antibiotic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Brem, S. S. Van Berkel, D. Zollman, S. Y. Lee, O. Gileadi, P. J. Mchugh, T. R. Walsh, M. A. Mcdonough, C. J. Schofield
Structural Basis Of Metallo-Beta-Lactamase Inhibition By Captopril Stereoisomers.
Antimicrob. Agents Chemother. V. 60 142 2015
PubMed-ID: 26482303 | Reference-DOI: 10.1128/AAC.01335-15

Molecule 1 - BETA-LACTAMASE IMP-1
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Expression System Vector	:	PET-26B
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SERRATIA MARCESCENS
	Organism Taxid	:	615
	Other Details	:	PLASMID DERIVED NON-GENOMIC.
	Synonym	:	BLAIMP, BETA-LACTAMASE TYPE II, PENICILLINASE

		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, 7)

No.	Name	Count	Type	Full Name
1	MCO	1	Ligand/Ion	1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	MCO	1	Ligand/Ion	1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MCO	-1	Ligand/Ion	1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID
2	SO4	-1	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:95 , HIS A:97 , HIS A:157 , ZN A:301 , MCO A:305	BINDING SITE FOR RESIDUE ZN A 300
2	AC2	SOFTWARE	ASP A:99 , CYS A:176 , HIS A:215 , ZN A:300 , MCO A:305	BINDING SITE FOR RESIDUE ZN A 301
3	AC3	SOFTWARE	TRP A:46 , VAL A:49 , ASP A:99 , HIS A:157 , LYS A:179 , GLY A:184 , ASN A:185 , HIS A:215 , ZN A:300 , ZN A:301 , HOH A:2168	BINDING SITE FOR RESIDUE MCO A 305
4	AC4	SOFTWARE	GLU A:32 , VAL A:34 , VAL A:56 , LEU A:57 , GLU A:168 , ARG A:169	BINDING SITE FOR RESIDUE SO4 A 310
5	AC5	SOFTWARE	TRP A:80 , ARG A:84 , GLU A:168 , ARG A:169 , HOH A:2199 , HOH A:2200 , HOH A:2201	BINDING SITE FOR RESIDUE SO4 A 311
6	AC6	SOFTWARE	ASP B:99 , CYS B:176 , HIS B:215 , ZN B:301 , HOH B:2005	BINDING SITE FOR RESIDUE ZN B 300
7	AC7	SOFTWARE	HIS B:95 , HIS B:97 , HIS B:157 , ZN B:300 , HOH B:2005	BINDING SITE FOR RESIDUE ZN B 301

(no "SS Bond" information available for 4C1G)

(no "Cis Peptide Bond" information available for 4C1G)

(no "SAP(SNP)/Variant" information available for 4C1G)

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_SERMA	92-111	2	A:92-111 B:92-111
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLAB_SERMA	167-179	2	A:167-179 B:167-179

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_SERMA	92-111	1	A:92-111 -
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLAB_SERMA	167-179	1	A:167-179 -

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_SERMA	92-111	1	- B:92-111
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLAB_SERMA	167-179	1	- B:167-179

(no "Exon" information available for 4C1G)

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 BLAB_SERMA | P52699 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:219
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
           BLAB_SERMA    21 SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 239
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------BETA_LACTAMASE_B_1  -------------------------------------------------------BETA_LACTAMAS------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c1g A  21 SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 239
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with BLAB_SERMA | P52699 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           BLAB_SERMA    22 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNES 238
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh....eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------BETA_LACTAMASE_B_1  -------------------------------------------------------BETA_LACTAMAS----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c1g B  22 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNES 238
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231

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 '\|'

(no "SCOP Domain" information available for 4C1G)

(no "CATH Domain" information available for 4C1G)

(no "Pfam Domain" information available for 4C1G)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BLAB_SERMA | P52699)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4c1g)

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

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	4c1g
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	BLAB_SERMA \| P52699	:	1dd6 1jje 1jjt 1vgn 1wuo 1wup 2doo 4c1f 5ev6 5ev8 5ewa 5hh4

4bz3	CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE VIM-2
4c09	CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE BCII WITH L-CAPTOPRIL
4c1c	CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE BCII WITH D-CAPTOPRIL
4c1d	CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE VIM-2 WITH L-CAPTOPRIL
4c1e	CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE VIM-2 WITH D-CAPTOPRIL
4c1f	CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE IMP-1 WITH L-CAPTOPRIL
4c1h	CRYSTAL STRUCTURE OF A BETA LACTAMASE IN COMPLEX WITH AN INHIBITOR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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