2Y91 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CLASS A BETA-LACTAMASE FROM BACILLUS LICHENIFORMIS BS3 WITH CLAVULANIC ACID

Authors :   P. Power, E. Sauvage, R. Herman, F. Kerff, P. Charlier

Date :   11 Feb 11 (Deposition) - 22 Feb 12 (Release) - 26 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   P. Power, P. Mercuri, R. Herman, F. Kerff, G. Gutkind, G. Dive, M. Galleni, P. Charlier, E. Sauvage
Novel Fragments Of Clavulanate Observed In The Structure Of The Class A Beta-Lactamase From Bacillus Licheniformis Bs3.
J. Antimicrob. Chemother. V. 67 2379 2012
PubMed-ID: 22773738 | Reference-DOI: 10.1093/JAC/DKS231

Molecule 1 - BETA-LACTAMASE
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Organism Scientific	:	BACILLUS LICHENIFORMIS
	Organism Taxid	:	1402
	Strain	:	BS3

		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 (4, 7)

No.	Name	Count	Type	Full Name
1	1X6	2	Mod. Amino Acid	O-[(2E)-3-AMINOPROP-2-ENOYL]-L-SERINE
2	98J	3	Ligand/Ion	5-HYDROXY-3-OXOPENTANOIC ACID
3	CIT	1	Ligand/Ion	CITRIC ACID
4	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	1X6	1	Mod. Amino Acid	O-[(2E)-3-AMINOPROP-2-ENOYL]-L-SERINE
2	98J	1	Ligand/Ion	5-HYDROXY-3-OXOPENTANOIC ACID
3	CIT	1	Ligand/Ion	CITRIC ACID
4	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	1X6	1	Mod. Amino Acid	O-[(2E)-3-AMINOPROP-2-ENOYL]-L-SERINE
2	98J	2	Ligand/Ion	5-HYDROXY-3-OXOPENTANOIC ACID
3	CIT	-1	Ligand/Ion	CITRIC ACID
4	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	1X6 A:70 , SER A:130 , LYS A:234 , THR A:235 , GLY A:236 , ARG A:244 , HOH A:2098	BINDING SITE FOR RESIDUE 98J A1293
2	AC2	SOFTWARE	ASN A:161 , GLU A:163 , GLU A:176 , THR A:177 , GLN A:178 , HOH A:2077 , GLU B:171 , ASN B:173 , LYS B:270 , HOH B:2094	BINDING SITE FOR RESIDUE CIT A1294
3	AC3	SOFTWARE	ARG A:65 , ASN A:173 , PRO A:174 , GLY A:175 , GLU A:176	BINDING SITE FOR RESIDUE PGE A1295
4	AC4	SOFTWARE	1X6 B:70 , SER B:130 , LYS B:234 , THR B:235 , GLY B:236 , ARG B:244	BINDING SITE FOR RESIDUE 98J B1293
5	AC5	SOFTWARE	ASN A:173 , HOH A:2076 , GLU B:176 , THR B:177 , GLN B:178 , HOH B:2116	BINDING SITE FOR RESIDUE 98J B1294

(no "SS Bond" information available for 2Y91)

Asymmetric Unit

No.	Residues
1	Glu A:166	-	Pro A:167
2	Glu B:166	-	Pro B:167

(no "SAP(SNP)/Variant" information available for 2Y91)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_A	PS00146	Beta-lactamase class-A active site.	BLAC_BACLI	82-97	2	A:66-81 B:66-81

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_A	PS00146	Beta-lactamase class-A active site.	BLAC_BACLI	82-97	1	A:66-81 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_A	PS00146	Beta-lactamase class-A active site.	BLAC_BACLI	82-97	1	- B:66-81

(no "Exon" information available for 2Y91)

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:257
 aligned with BLAC_BACLI | P00808 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:257
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       
           BLAC_BACLI    47 KDDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 303
               SCOP domains d2y91a_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh.hhhhh.ee..hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------BETA_LACTAMASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y91 A  30 KDDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFAsTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 291
                                    39        49       |60        70        80  ||    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     ||243       254       264       274       284       
                                                      57|         70-1X6       83|                                                                                                                                                     238|         252|                                     
                                                       59                       86                                                                                                                                                      240          254

Chain A from PDB  Type:PROTEIN  Length:257
 aligned with P94458_BACLI | P94458 from UniProtKB/TrEMBL  Length:265

    Alignment length:257
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       
         P94458_BACLI     5 KDDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 261
               SCOP domains d2y91a_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh.hhhhh.ee..hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y91 A  30 KDDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFAsTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 291
                                    39        49       |60        70        80  ||    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     ||243       254       264       274       284       
                                                      57|         70-1X6       83|                                                                                                                                                     238|         252|                                     
                                                       59                       86                                                                                                                                                      240          254

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with BLAC_BACLI | P00808 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:257
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       
           BLAC_BACLI    47 KDDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 303
               SCOP domains d2y91b_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh.hhhhh.ee............hhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------BETA_LACTAMASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y91 B  30 KDDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFAsTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 291
                                    39        49       |60        70        80  ||    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     ||243       254       264       274       284       
                                                      57|         70-1X6       83|                                                                                                                                                     238|         252|                                     
                                                       59                       86                                                                                                                                                      240          254

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with P94458_BACLI | P94458 from UniProtKB/TrEMBL  Length:265

    Alignment length:257
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       
         P94458_BACLI     5 KDDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 261
               SCOP domains d2y91b_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh.hhhhh.ee............hhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y91 B  30 KDDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFAsTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 291
                                    39        49       |60        70        80  ||    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     ||243       254       264       274       284       
                                                      57|         70-1X6       83|                                                                                                                                                     238|         252|                                     
                                                       59                       86                                                                                                                                                      240          254

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: Multi-domain proteins (alpha and beta) (2421)

Fold: beta-lactamase/transpeptidase-like (515)

Superfamily: beta-lactamase/transpeptidase-like (515)

Family: beta-Lactamase/D-ala carboxypeptidase (411)

Protein domain: automated matches (81)

Bacillus licheniformis [TaxId: 1402] (6)

1a	d2y91a_	A:
1b	d2y91b_	B:

(no "CATH Domain" information available for 2Y91)

(no "Pfam Domain" information available for 2Y91)

Asymmetric Unit(hide GO term definitions)

Chain A,B (P94458_BACLI | P94458)

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.
biological process
	GO:0030655	beta-lactam antibiotic catabolic process	The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
	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.

Chain A,B (BLAC_BACLI | P00808)

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.
biological process
	GO:0030655	beta-lactam antibiotic catabolic process	The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	Ligands, Modified Residues, Ions
		1X6	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		98J	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Glu A:166 - Pro A:167	[ RasMol ]
		Glu B:166 - Pro B:167	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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	2y91
		Family and Domain Information	:	ProDom \| SYSTERS
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	BLAC_BACLI \| P00808
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	P94458_BACLI \| P94458
		Comparative Protein Structure Models	:	ModBase
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	3.5.2.6
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		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	BLAC_BACLI \| P00808	:	1i2s 1i2w 1mbl 1w7f 2blm 2wk0 3b3x 3ly3 3ly4 3m2j 3m2k 3sh7 3sh8 3sh9 3soi 4blm 4m3k 4n1h 4n92 4n9k 4n9l 5ghx 5ghy 5ghz
	P94458_BACLI \| P94458	:	1w7f 2wk0 3b3x
UniProtKB/TrEMBL
	P94458_BACLI \| P94458	:	2x71 4a5r

2x71	STRUCTURAL BASIS FOR THE INTERACTION OF LACTIVICINS WITH SERINE BETA-LACTAMASES

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 10)

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