2QDT - JenaLib

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Title :   STRUCTURAL BASIS FOR THE BROAD-SPECTRUM INHIBITION OF METALLO-{BETA}-LACTAMASES: L1- IS38 COMPLEX

Authors :   G. Garau, O. Dideberg

Date :   21 Jun 07 (Deposition) - 28 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Hydrolase, Zn, Metallo, Lactamase, Inhibitor, L1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. M. Lienard, G. Garau, L. Horsfall, A. I. Karsisiotis, C. Damblon, P. Lassaux, C. Papamicael, G. C. Roberts, M. Galleni, O. Dideberg, J. M. Frere, C. J. Schofield
Structural Basis For The Broad-Spectrum Inhibition Of Metallo-Beta-Lactamases By Thiols.
Org. Biomol. Chem. V. 6 2282 2008
PubMed-ID: 18563261 | Reference-DOI: 10.1039/B802311E
(for further references see the PDB file header)

Molecule 1 - METALLO-BETA-LACTAMASE L1
	Chains	:	A
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET26
	Expression System Strain	:	BL21(DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	L1
	Organism Scientific	:	STENOTROPHOMONAS MALTOPHILIA
	Organism Taxid	:	40324
	Strain	:	IID 1275
	Synonym	:	BETA-LACTAMASE TYPE II, PENICILLINASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	I38	1	Ligand/Ion	N-(3-MERCAPTOPROPANOYL)-D-ALANINE
2	SO4	3	Ligand/Ion	SULFATE ION
3	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	I38	2	Ligand/Ion	N-(3-MERCAPTOPROPANOYL)-D-ALANINE
2	SO4	6	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	I38	2	Ligand/Ion	N-(3-MERCAPTOPROPANOYL)-D-ALANINE
2	SO4	6	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:84 , HIS A:86 , HIS A:160 , I38 A:501	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	ASP A:88 , HIS A:89 , HIS A:225 , I38 A:501	BINDING SITE FOR RESIDUE ZN A 402
3	AC3	SOFTWARE	ASP A:28 , HIS A:29	BINDING SITE FOR RESIDUE ZN A 403
4	AC4	SOFTWARE	ARG A:137 , VAL A:144 , ILE A:145 , THR A:146 , HOH A:730	BINDING SITE FOR RESIDUE SO4 A 602
5	AC5	SOFTWARE	ARG A:173 , ARG A:214 , ALA A:237 , ARG A:238 , ALA A:239 , GLY A:240 , ALA A:241 , LYS A:247 , HOH A:750	BINDING SITE FOR RESIDUE SO4 A 603
6	AC6	SOFTWARE	GLU A:95 , ARG A:98 , ARG A:99 , HOH A:834	BINDING SITE FOR RESIDUE SO4 A 604
7	AC7	SOFTWARE	TYR A:11 , ASP A:88 , HIS A:160 , SER A:187 , PRO A:189 , ZN A:401 , ZN A:402 , HOH A:606 , HOH A:610 , HOH A:812	BINDING SITE FOR RESIDUE I38 A 501

Asymmetric Unit

No.	Residues
1	A:218	-	A:246

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_B_1	PS00743	Beta-lactamases class B signature 1.	BLA1_STEMA	102-122	1	A:81-101

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_B_1	PS00743	Beta-lactamases class B signature 1.	BLA1_STEMA	102-122	2	A:81-101

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_B_1	PS00743	Beta-lactamases class B signature 1.	BLA1_STEMA	102-122	2	A:81-101

(no "Exon" information available for 2QDT)

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:266
 aligned with BLA1_STEMA | P52700 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:266
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      
           BLA1_STEMA    23 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 288
               SCOP domains d2qdta_ A: Zn metallo-beta-lactamase                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2qdtA00 A:2-267 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------Lactamase_B-2qdtA01 A:34-225                                                                                                                                                                    ------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhh....ee....eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhh..eeeehhhhhhhhhh....................ee.....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhhh...eee..hhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------BETA_LACTAMASE_B_1   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qdt A   2 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 267
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

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( (-)

)

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)

Xanthomonas maltophilia [TaxId: 40324] (12)

d2qdta_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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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)

Stenotrophomonas maltophilia. Organism_taxid: 40324. Strain: iid 1275. (10)

2qdtA00

A:2-267

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Metallo-HOrase (67)

Family: Lactamase_B (53)

Stenotrophomonas maltophilia (Pseudomonas maltophilia) (Xanthomonas maltophilia) (4)

Lactamase_B-2qdtA01

A:34-225

Asymmetric Unit(hide GO term definitions)

Chain A (BLA1_STEMA | P52700)

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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Description

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Ligands, Modified Residues, Ions (3, 7)

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SS Bonds (1, 1)

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