1WUO - JenaLib

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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)

Title :   CRYSTAL STRUCTURE OF METALLO-BETA-LACTAMASE IMP-1 MUTANT (D81A)

Authors :   Y. Yamaguchi, Y. Yamagata, M. Goto

Date :   08 Dec 04 (Deposition) - 29 Mar 05 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

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

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

Reference :   Y. Yamaguchi, T. Kuroki, H. Yasuzawa, T. Higashi, W. Jin, A. Kawanami, Y. Yamagata, Y. Arakawa, M. Goto, H. Kurosaki
Probing The Role Of Asp-120(81) Of Metallo-Beta-Lactamase (Imp-1) By Site-Directed Mutagenesis, Kinetic Studies, And X-Ray Crystallography.
J. Biol. Chem. V. 280 20824 2005
PubMed-ID: 15788415 | Reference-DOI: 10.1074/JBC.M414314200

Molecule 1 - BETA-LACTAMASE IMP-1
	Chains	:	A, B, C, D
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKF19K-IMP
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BLAIMP-1
	Mutation	:	YES
	Organism Scientific	:	SERRATIA MARCESCENS
	Organism Taxid	:	615
	Strain	:	TN9106
	Synonym	:	IMP-1 METALLO-BETA-LACTAMASE, BETA-LACTAMASE, TYPE II, PENICILLINASE, BLAIMP

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	ACY	4	Ligand/Ion	ACETIC ACID
2	CSD	4	Mod. Amino Acid	3-SULFINOALANINE
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	CSD	1	Mod. Amino Acid	3-SULFINOALANINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	CSD	1	Mod. Amino Acid	3-SULFINOALANINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	CSD	1	Mod. Amino Acid	3-SULFINOALANINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	CSD	1	Mod. Amino Acid	3-SULFINOALANINE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:77 , HIS A:79 , HIS A:139 , CSD A:158 , ACY A:401	BINDING SITE FOR RESIDUE ZN A 301
2	AC2	SOFTWARE	HIS B:77 , HIS B:79 , HIS B:139 , CSD B:158 , ACY B:402	BINDING SITE FOR RESIDUE ZN B 302
3	AC3	SOFTWARE	HIS C:77 , HIS C:79 , HIS C:139 , CSD C:158 , ACY C:403	BINDING SITE FOR RESIDUE ZN C 303
4	AC4	SOFTWARE	HIS D:77 , HIS D:79 , HIS D:139 , CSD D:158 , ACY D:404	BINDING SITE FOR RESIDUE ZN D 304
5	AC5	SOFTWARE	HIS A:77 , HIS A:79 , ALA A:81 , HIS A:139 , CSD A:158 , ZN A:301 , HOH A:438	BINDING SITE FOR RESIDUE ACY A 401
6	AC6	SOFTWARE	HIS B:79 , HIS B:139 , CSD B:158 , ZN B:302 , HOH B:413	BINDING SITE FOR RESIDUE ACY B 402
7	AC7	SOFTWARE	HIS C:77 , HIS C:79 , HIS C:139 , CSD C:158 , ZN C:303 , HOH C:404 , HOH C:445	BINDING SITE FOR RESIDUE ACY C 403
8	AC8	SOFTWARE	HIS D:77 , HIS D:79 , ALA D:81 , HIS D:139 , CSD D:158 , ZN D:304 , HOH D:405 , HOH D:406	BINDING SITE FOR RESIDUE ACY D 404

(no "SS Bond" information available for 1WUO)

(no "Cis Peptide Bond" information available for 1WUO)

(no "SAP(SNP)/Variant" information available for 1WUO)

Asymmetric Unit (2, 8)

	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	4	A:74-93 B:74-93 C:74-93 D:74-93
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLAB_SERMA	167-179	4	A:149-161 B:149-161 C:149-161 D:149-161

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:74-93 - - -
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLAB_SERMA	167-179	1	A:149-161 - - -

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:74-93 - -
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLAB_SERMA	167-179	1	- B:149-161 - -

Biological Unit 3 (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	- - C:74-93 -
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLAB_SERMA	167-179	1	- - C:149-161 -

Biological Unit 4 (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	- - - D:74-93
2	BETA_LACTAMASE_B_2	PS00744	Beta-lactamases class B signature 2.	BLAB_SERMA	167-179	1	- - - D:149-161

(no "Exon" information available for 1WUO)

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 d1wuoa_ A: Zn metallo-beta-lactamase                                                                                                                                                                                        SCOP domains
               CATH domains 1wuoA00 A:3-221 Metallo-beta-lactamase, chain A                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeeeeee.....eeeeeeeeee...eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeee.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------BETA_LACTAMASE_B_1  -------------------------------------------------------BETA_LACTAMAS------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wuo A   3 SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSASTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGcFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 221
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     | 162       172       182       192       202       212         
                                                                                                                                                                                     158-CSD

Chain B 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 d1wuob_ B: Zn metallo-beta-lactamase                                                                                                                                                                                        SCOP domains
               CATH domains 1wuoB00 B:3-221 Metallo-beta-lactamase, chain A                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeeeeee.....eeeeeeeeee...eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeee.................hhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------BETA_LACTAMASE_B_1  -------------------------------------------------------BETA_LACTAMAS------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wuo B   3 SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSASTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGcFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 221
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     | 162       172       182       192       202       212         
                                                                                                                                                                                     158-CSD

Chain C 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 d1wuoc_ C: Zn metallo-beta-lactamase                                                                                                                                                                                        SCOP domains
               CATH domains 1wuoC00 C:3-221 Metallo-beta-lactamase, chain A                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeeeeee.....eeeeeeeeee...eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...ee.hhhhhhhhhhh............eeeee...eeee...........eeee....eeeee.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------BETA_LACTAMASE_B_1  -------------------------------------------------------BETA_LACTAMAS------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wuo C   3 SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSASTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGcFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 221
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     | 162       172       182       192       202       212         
                                                                                                                                                                                     158-CSD

Chain D 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 d1wuod_ D: Zn metallo-beta-lactamase                                                                                                                                                                                        SCOP domains
               CATH domains 1wuoD00 D:3-221 Metallo-beta-lactamase, chain A                                                                                                                                                                             CATH domains
           Pfam domains (1) -------------------------Lactamase_B-1wuoD01 D:28-211                                                                                                                                                            ---------- Pfam domains (1)
           Pfam domains (2) -------------------------Lactamase_B-1wuoD02 D:28-211                                                                                                                                                            ---------- Pfam domains (2)
           Pfam domains (3) -------------------------Lactamase_B-1wuoD03 D:28-211                                                                                                                                                            ---------- Pfam domains (3)
           Pfam domains (4) -------------------------Lactamase_B-1wuoD04 D:28-211                                                                                                                                                            ---------- Pfam domains (4)
         Sec.struct. author .....eeeeee..eeeeeeeee.....eeeeeeeeee...eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeee.................hhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------BETA_LACTAMASE_B_1  -------------------------------------------------------BETA_LACTAMAS------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wuo D   3 SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSASTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGcFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 221
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     | 162       172       182       192       202       212         
                                                                                                                                                                                     158-CSD

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)

Serratia marcescens [TaxId: 615] (3)

1a	d1wuoa_	A:
1b	d1wuob_	B:
1c	d1wuoc_	C:
1d	d1wuod_	D:

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)

Serratia marcescens. Organism_taxid: 615. Strain: tn9106. (2)

1a	1wuoA00	A:3-221
1b	1wuoB00	B:3-221
1c	1wuoC00	C:3-221
1d	1wuoD00	D:3-221

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Metallo-HOrase (67)

Family: Lactamase_B (53)

Serratia marcescens (3)

1a	Lactamase_B-1wuoD01	D:28-211
1b	Lactamase_B-1wuoD02	D:28-211
1c	Lactamase_B-1wuoD03	D:28-211
1d	Lactamase_B-1wuoD04	D:28-211

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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).

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wuo)

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	1wuo
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	3.5.2.6
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	BLAB_SERMA \| P52699	:	1dd6 1jje 1jjt 1vgn 1wup 2doo 4c1f 4c1g 5ev6 5ev8 5ewa 5hh4

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

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