3LCE - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF OXA-10 BETA-LACTAMASE COVALENTLY BOUND TO CYCLOBUTANONE BETA-LACTAM MIMIC

Authors :   M. Gretes, N. C. J. Strynadka

Date :   10 Jan 10 (Deposition) - 09 Mar 10 (Release) - 09 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Beta-Lactamase, Beta-Lactamase Inhibitor, Beta-Lactam Mimic, Cyclobutanone, Hemiketal, Antibiotic Resistance, Disulfide Bond, Hydrolase, Plasmid, Transposable Element (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. W. Johnson, M. Gretes, V. J. Goodfellow, L. Marrone, M. L. Heynen, N. C. Strynadka, G. I. Dmitrienko
Cyclobutanone Analogues Of Beta-Lactams Revisited: Insights Into Conformational Requirements For Inhibition Of Serine- And Metallo-Beta-Lactamases.
J. Am. Chem. Soc. V. 132 2558 2010
PubMed-ID: 20141132 | Reference-DOI: 10.1021/JA9086374

Molecule 1 - BETA-LACTAMASE OXA-10
	Chains	:	A, B, C, D
	EC Number	:	3.5.2.6
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Strain	:	AH
	Synonym	:	BETA-LACTAMASE PSE-2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 19)

No.	Name	Count	Type	Full Name
1	GOL	11	Ligand/Ion	GLYCEROL
2	KCX	4	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	LCE	2	Ligand/Ion	(1S,3S,4S,5S)-7,7-DICHLORO-3-METHOXY-2-THIABICYCLO[3.2.0]HEPTAN-6-ONE-4-CARBOXYLIC ACID
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	LCE	1	Ligand/Ion	(1S,3S,4S,5S)-7,7-DICHLORO-3-METHOXY-2-THIABICYCLO[3.2.0]HEPTAN-6-ONE-4-CARBOXYLIC ACID
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (4, 11)

No.	Name	Count	Type	Full Name
1	GOL	7	Ligand/Ion	GLYCEROL
2	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	LCE	1	Ligand/Ion	(1S,3S,4S,5S)-7,7-DICHLORO-3-METHOXY-2-THIABICYCLO[3.2.0]HEPTAN-6-ONE-4-CARBOXYLIC ACID
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:80 , ARG A:131 , LYS A:134 , TYR A:135 , HOH A:854	BINDING SITE FOR RESIDUE GOL A 1
02	AC2	SOFTWARE	THR A:206 , ARG A:250 , LYS A:251 , LCE A:269	BINDING SITE FOR RESIDUE GOL A 267
03	AC3	SOFTWARE	ALA A:197 , PRO A:198 , GLU A:199 , TYR A:200 , GLU A:229 , HOH A:284 , THR C:107 , ARG C:109	BINDING SITE FOR RESIDUE GOL A 268
04	AC4	SOFTWARE	ALA A:66 , SER A:67 , KCX A:70 , SER A:115 , VAL A:117 , LEU A:155 , THR A:206 , GLY A:207 , PHE A:208 , ARG A:250 , GOL A:267 , HOH A:334	BINDING SITE FOR RESIDUE LCE A 269
05	AC5	SOFTWARE	ARG B:160 , HOH B:638	BINDING SITE FOR RESIDUE GOL B 1
06	AC6	SOFTWARE	ARG B:131 , LYS B:134 , TYR B:135	BINDING SITE FOR RESIDUE GOL B 267
07	AC7	SOFTWARE	ALA B:197 , PRO B:198 , GLU B:199 , TYR B:200 , GLU B:229 , HOH B:407 , THR D:107 , ARG D:109	BINDING SITE FOR RESIDUE GOL B 268
08	AC8	SOFTWARE	SER B:181 , LYS B:182 , HOH B:609	BINDING SITE FOR RESIDUE GOL B 269
09	AC9	SOFTWARE	ALA B:66 , SER B:67 , KCX B:70 , SER B:115 , VAL B:117 , THR B:206 , GLY B:207 , PHE B:208 , ARG B:250	BINDING SITE FOR RESIDUE LCE B 270
10	BC1	SOFTWARE	LYS B:95 , SER C:67 , SER C:115 , LYS C:205 , THR C:206 , GLY C:207 , PHE C:208 , ARG C:250 , HOH C:280 , HOH C:291 , HOH C:294	BINDING SITE FOR RESIDUE PO4 C 1
11	BC2	SOFTWARE	THR A:107 , ARG A:109 , HOH C:7 , ALA C:197 , PRO C:198 , GLU C:199 , TYR C:200 , GLU C:227 , GLU C:229 , HOH C:336	BINDING SITE FOR RESIDUE GOL C 267
12	BC3	SOFTWARE	LYS A:95 , SER D:67 , SER D:115 , LYS D:205 , THR D:206 , GLY D:207 , PHE D:208 , ARG D:250 , HOH D:286 , HOH D:758 , HOH D:834	BINDING SITE FOR RESIDUE PO4 D 2
13	BC4	SOFTWARE	HOH D:844	BINDING SITE FOR RESIDUE GOL D 1
14	BC5	SOFTWARE	HOH B:13 , THR B:107 , ARG B:109 , ALA D:197 , PRO D:198 , GLU D:199 , TYR D:200 , GLU D:227 , GLU D:229 , HOH D:305	BINDING SITE FOR RESIDUE GOL D 267
15	BC6	SOFTWARE	ASN D:145 , SER D:147 , GLN D:158 , HOH D:620	BINDING SITE FOR RESIDUE GOL D 268

Asymmetric Unit

No.	Residues
1	A:44	-	A:51
2	B:44	-	B:51
3	C:44	-	C:51
4	D:44	-	D:51

Asymmetric Unit

No.	Residues
1	Ile A:264	-	Gly A:265

(no "SAP(SNP)/Variant" information available for 3LCE)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_D	PS00337	Beta-lactamase class-D active site.	BLO10_PSEAI	65-75	4	A:65-75 B:65-75 C:65-75 D:65-75

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_D	PS00337	Beta-lactamase class-D active site.	BLO10_PSEAI	65-75	2	A:65-75 - C:65-75 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_D	PS00337	Beta-lactamase class-D active site.	BLO10_PSEAI	65-75	2	- B:65-75 - D:65-75

(no "Exon" information available for 3LCE)

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:245
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:245
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
          BLO10_PSEAI    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
               SCOP domains d3lcea_ A: Class D beta-lactamase                                                                                                                                                                                                                     SCOP domains
               CATH domains 3lceA00 A:21-265 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhh...eeeeeee.....eee...hhhhh...hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------BETA_LACTAM---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lce A  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
                                                                            70-KCX

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:245
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
          BLO10_PSEAI    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
               SCOP domains d3lceb_ B: Class D beta-lactamase                                                                                                                                                                                                                     SCOP domains
               CATH domains 3lceB00 B:21-265 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhh....eeeeeee.....eee.hhhhhh....hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------BETA_LACTAM---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lce B  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
                                                                            70-KCX

Chain C from PDB  Type:PROTEIN  Length:246
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:246
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
          BLO10_PSEAI    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG 266
               SCOP domains d3lcec_ C: Class D beta-lactamase                                                                                                                                                                                                                      SCOP domains
               CATH domains 3lceC00 C:21-266 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.hhhhhhhhh....eeeeeee.....eee.hhhhhhhee.hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh...eehhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lce C  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG 266
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
                                                                            70-KCX

Chain D from PDB  Type:PROTEIN  Length:246
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:246
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
          BLO10_PSEAI    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG 266
               SCOP domains d3lced_ D: Class D beta-lactamase                                                                                                                                                                                                                      SCOP domains
               CATH domains 3lceD00 D:21-266 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhh..eeeeeee.....eee.hhhhhh.ee.hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh...eehhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lce D  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG 266
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
                                                                            70-KCX

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: Class D beta-lactamase (32)

Pseudomonas aeruginosa, OXA-10 [TaxId: 287] (25)

1a	d3lcea_	A:
1b	d3lceb_	B:
1c	d3lcec_	C:
1d	d3lced_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Beta-lactamase (339)

Homologous Superfamily: DD-peptidase/beta-lactamase superfamily (335)

Pseudomonas aeruginosa. Organism_taxid: 287. Strain: ah (1)

1a	3lceC00	C:21-266
1b	3lceD00	D:21-266
1c	3lceA00	A:21-265
1d	3lceB00	B:21-265

(no "Pfam Domain" information available for 3LCE)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (BLO10_PSEAI | P14489)

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:0008658	penicillin binding	Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ile A:264 - Gly A:265	[ RasMol ]

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	3lce
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(no "Related Entries Specified in the PDB File" available for 3LCE)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 19)

Sites (15, 15)

SS Bonds (4, 4)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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Gene Ontology (5, 5)

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