2QJS - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   STENOTROPHOMONAS MALTOPHILIA L1 METALLO-BETA-LACTAMASE ASP-120 ASN MUTANT

Authors :   J. Crisp, R. Conners, J. Spencer

Date :   09 Jul 07 (Deposition) - 21 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)
Biol. Unit 4: C  (1x)
Biol. Unit 5: D  (1x)

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

Reference :   J. Crisp, R. Conners, J. D. Garrity, A. L. Carenbauer, M. W. Crowder, J. Spencer
Structural Basis For The Role Of Asp-120 In Metallo-Beta-Lactamases
Biochemistry V. 46 10664 2007
PubMed-ID: 17715946 | Reference-DOI: 10.1021/BI700707U
(for further references see the PDB file header)

Molecule 1 - METALLO-BETA-LACTAMASE L1
	Chains	:	A, B, C, D
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUB5832
	Expression System Strain	:	BL21 (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET26B
	Gene	:	L1
	Mutation	:	YES
	Organism Scientific	:	STENOTROPHOMONAS MALTOPHILIA
	Organism Taxid	:	40324
	Strain	:	IID 1275
	Synonym	:	BETA-LACTAMASE TYPE II, PENICILLINASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B
Biological Unit 4 (1x)	:			C
Biological Unit 5 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	ZN	8	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

Biological Unit 3 (0, 0)

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

Biological Unit 4 (0, 0)

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

Biological Unit 5 (0, 0)

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

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:121 , HIS A:263 , ZN A:2002 , HOH A:2095 , HOH A:2096 , HOH A:2108	BINDING SITE FOR RESIDUE ZN A 2001
2	AC2	SOFTWARE	HIS A:116 , HIS A:118 , HIS A:196 , ZN A:2001 , HOH A:2095	BINDING SITE FOR RESIDUE ZN A 2002
3	AC3	SOFTWARE	HIS B:121 , HIS B:263 , HOH B:2084 , HOH B:2085	BINDING SITE FOR RESIDUE ZN B 2001
4	AC4	SOFTWARE	HIS B:116 , HIS B:118 , HIS B:196 , HOH B:2084	BINDING SITE FOR RESIDUE ZN B 2002
5	AC5	SOFTWARE	HIS C:121 , HIS C:263 , HOH C:2069 , HOH C:2070	BINDING SITE FOR RESIDUE ZN C 2001
6	AC6	SOFTWARE	HIS C:116 , HIS C:118 , HIS C:196 , HOH C:2069	BINDING SITE FOR RESIDUE ZN C 2002
7	AC7	SOFTWARE	HIS D:121 , HIS D:263 , HOH D:2093	BINDING SITE FOR RESIDUE ZN D 2001
8	AC8	SOFTWARE	HIS D:116 , HIS D:118 , HIS D:196	BINDING SITE FOR RESIDUE ZN D 2002

Asymmetric Unit

No.	Residues
1	A:256	-	A:290
2	B:256	-	B:290
3	C:256	-	C:290
4	D:256	-	D:290

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

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

Asymmetric Unit (1, 4)

	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	4	A:113-133 B:113-133 C:113-133 D:113-133

Biological Unit 1 (1, 4)

	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	4	A:113-133 B:113-133 C:113-133 D:113-133

Biological Unit 2 (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:113-133 - - -

Biological Unit 3 (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	- B:113-133 - -

Biological Unit 4 (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	- - C:113-133 -

Biological Unit 5 (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	- - - D:113-133

(no "Exon" information available for 2QJS)

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:248
 aligned with BLA1_STEMA | P52700 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:248
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        
           BLA1_STEMA    41 PMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 288
               SCOP domains d2qjsa_ A: Zn metallo-beta-lactamase                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhh..eeeehhhhhhhhhh....................ee.....eeee..eeeeeee........eeeeee........eeee..................hhhhhhhhhhhhhhh....eee..hhhhh..hhhhh........hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------BETA_LACTAMASE_B_1   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qjs A  24 PMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHANHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 311
                                ||  51     || 69      ||80      ||91       101       111       121       131       141       151     ||163  ||   174       184       195       205       215       226       236       246     ||257       267       277||     293       303        
                               28|        57|        76|       87|                                                                 157|   166|                     192|                           224|                       252|                     278|                          
                                47         66         78        89                                                                  160    168                      194                            226                        254                      285

Chain B from PDB  Type:PROTEIN  Length:248
 aligned with BLA1_STEMA | P52700 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:248
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        
           BLA1_STEMA    41 PMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 288
               SCOP domains d2qjsb_ B: Zn metallo-beta-lactamase                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eee........eeee....eeee...hhhhhhhhhhhhhh...hhh.eeeee....hhhhhhhhhhhhhhh..eeeehhhhhhhhhh....................ee.....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhh....eee..hhhhhh..............hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------BETA_LACTAMASE_B_1   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qjs B  24 PMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHANHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 311
                                ||  51     || 69      ||80      ||91       101       111       121       131       141       151     ||163  ||   174       184       195       205       215       226       236       246     ||257       267       277||     293       303        
                               28|        57|        76|       87|                                                                 157|   166|                     192|                           224|                       252|                     278|                          
                                47         66         78        89                                                                  160    168                      194                            226                        254                      285

Chain C from PDB  Type:PROTEIN  Length:248
 aligned with BLA1_STEMA | P52700 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:248
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        
           BLA1_STEMA    41 PMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 288
               SCOP domains d2qjsc_ C: Zn metallo-beta-lactamase                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee........eeeee..eeeee...hhhhhhhhhhhhhh...hhh.eeeee....hhhhhhhhhhhhhhh..eeeeehhhhhhhhh....................eee....eee....eeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhh....eee..hhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------BETA_LACTAMASE_B_1   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qjs C  24 PMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHANHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 311
                                ||  51     || 69      ||80      ||91       101       111       121       131       141       151     ||163  ||   174       184       195       205       215       226       236       246     ||257       267       277||     293       303        
                               28|        57|        76|       87|                                                                 157|   166|                     192|                           224|                       252|                     278|                          
                                47         66         78        89                                                                  160    168                      194                            226                        254                      285

Chain D from PDB  Type:PROTEIN  Length:248
 aligned with BLA1_STEMA | P52700 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:248
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        
           BLA1_STEMA    41 PMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 288
               SCOP domains d2qjsd_ D: Zn metallo-beta-lactamase                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------Lactamase_B-2qjsD01 D:56-263                                                                                                                                                                    ------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------Lactamase_B-2qjsD02 D:56-263                                                                                                                                                                    ------------------------------------------ Pfam domains (2)
           Pfam domains (3) --------------Lactamase_B-2qjsD03 D:56-263                                                                                                                                                                    ------------------------------------------ Pfam domains (3)
           Pfam domains (4) --------------Lactamase_B-2qjsD04 D:56-263                                                                                                                                                                    ------------------------------------------ Pfam domains (4)
         Sec.struct. author ....ee....eee........eeeee..eeeee......hhhhhhhhhhhhh.hhh.eeeee....hhhhhhhhhhhhhhh..eeeehhhhhhhhhh....................ee.....eeee..eeeeeee........eeeeeeeee..eeeeeeee.................hhhhhhhhhhhhhhh....eee..hhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------BETA_LACTAMASE_B_1   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qjs D  24 PMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHANHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 311
                                ||  51     || 69      ||80      ||91       101       111       121       131       141       151     ||163  ||   174       184       195       205       215       226       236       246     ||257       267       277||     293       303        
                               28|        57|        76|       87|                                                                 157|   166|                     192|                           224|                       252|                     278|                          
                                47         66         78        89                                                                  160    168                      194                            226                        254                      285

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)

Xanthomonas maltophilia [TaxId: 40324] (12)

1a	d2qjsa_	A:
1b	d2qjsb_	B:
1c	d2qjsc_	C:
1d	d2qjsd_	D:

(no "CATH Domain" information available for 2QJS)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Metallo-HOrase (67)

Family: Lactamase_B (53)

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

1a	Lactamase_B-2qjsD01	D:56-263
1b	Lactamase_B-2qjsD02	D:56-263
1c	Lactamase_B-2qjsD03	D:56-263
1d	Lactamase_B-2qjsD04	D:56-263

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (4, 4)

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