1K57 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   OXA 10 CLASS D BETA-LACTAMASE AT PH 6.0

Authors :   D. Golemi, L. Maveyraud, S. Vakulenko, J. P. Samama, S. Mobashery

Date :   10 Oct 01 (Deposition) - 07 Nov 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Beta-Lactamase, Antibiotic Resistance, Carbamylation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Golemi, L. Maveyraud, S. Vakulenko, J. P. Samama, S. Mobashery
Critical Involvement Of A Carbamylated Lysine In Catalytic Function Of Class D Beta-Lactamases.
Proc. Natl. Acad. Sci. Usa V. 98 14280 2001
PubMed-ID: 11724923 | Reference-DOI: 10.1073/PNAS.241442898
(for further references see the PDB file header)

Molecule 1 - BETA LACTAMASE OXA-10
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET24A
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Other Details	:	RESIDUE 70, KCX, IS CARBAMYLATED LYSINE
	Synonym	:	BETA-LACTAMASE PSE-2

Molecule 2 - BETA LACTAMASE OXA-10
	Chains	:	C, D
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET24A
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Other Details	:	RESIDUE 70, LYS, IS NOT CARBAMYLATED
	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 (2, 13)

No.	Name	Count	Type	Full Name
1	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
2	SO4	11	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
2	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:67 , SER A:115 , LYS A:205 , THR A:206 , GLY A:207 , PHE A:208 , ARG A:250 , HOH A:1021 , HOH A:1091	BINDING SITE FOR RESIDUE SO4 A 1001
02	AC2	SOFTWARE	ARG A:131 , LYS A:134 , TYR A:135 , HOH A:1122	BINDING SITE FOR RESIDUE SO4 A 1002
03	AC3	SOFTWARE	SER B:67 , SER B:115 , LYS B:205 , THR B:206 , GLY B:207 , PHE B:208 , ARG B:250 , HOH B:1020 , HOH B:1146	BINDING SITE FOR RESIDUE SO4 B 1003
04	AC4	SOFTWARE	LYS B:95 , THR C:206 , GLY C:207 , PHE C:208 , ARG C:250 , HOH C:1068 , HOH C:1099	BINDING SITE FOR RESIDUE SO4 C 1004
05	AC5	SOFTWARE	LYS A:95 , THR D:206 , GLY D:207 , PHE D:208 , ARG D:250 , HOH D:1130 , HOH D:1160 , HOH D:1171	BINDING SITE FOR RESIDUE SO4 D 1005
06	AC6	SOFTWARE	ARG B:131 , LYS B:134 , TYR B:135 , HOH B:1079 , HOH B:1156	BINDING SITE FOR RESIDUE SO4 B 1006
07	AC7	SOFTWARE	ARG B:160	BINDING SITE FOR RESIDUE SO4 B 1007
08	AC8	SOFTWARE	MET A:99 , LYS A:100 , GLN A:101	BINDING SITE FOR RESIDUE SO4 A 1008
09	AC9	SOFTWARE	SER C:67 , LYS C:70 , SER C:115 , ALA C:116 , HOH C:1022	BINDING SITE FOR RESIDUE SO4 C 1009
10	BC1	SOFTWARE	SER D:67 , LYS D:70 , SER D:115 , ALA D:116 , VAL D:117 , HOH D:1044 , HOH D:1137	BINDING SITE FOR RESIDUE SO4 D 1010
11	BC2	SOFTWARE	MET B:99 , LYS B:100 , GLN B:101	BINDING SITE FOR RESIDUE SO4 B 1011

Asymmetric Unit

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

(no "Cis Peptide Bond" information available for 1K57)

(no "SAP(SNP)/Variant" information available for 1K57)

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 1K57)

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:243
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:243
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   
          BLO10_PSEAI    22 ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
               SCOP domains d1k57a_ A: Class D beta-lactamase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1k57A00 A:22-264 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhh....eeeeeee.....eee.hhhhhh.ee.hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh...eehhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------BETA_LACTAM--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k57 A  22 ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   
                                                                           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 d1k57b_ B: Class D beta-lactamase                                                                                                                                                                                                                     SCOP domains
               CATH domains 1k57B00 B:21-265 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhh....eeeeeee.....eee.hhhhhh.ee.hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------BETA_LACTAM---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k57 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:241
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:244
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261    
          BLO10_PSEAI    22 ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
               SCOP domains d1k57c_ C: Class D beta-lactamase                                                                                                                                                                                                                    SCOP domains
               CATH domains 1k57C00 C:22-265 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhh....eeeeeee.....eee.hhhhhhh...hhhhhhhhhhhhhhhhh.......ee....---.hhhhhh.eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------BETA_LACTAM---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k57 C  22 ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDG---AMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
                                    31        41        51        61        71        81        91  |   |101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261    
                                                                                                   94  98

Chain D from PDB  Type:PROTEIN  Length:240
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:245
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     
          BLO10_PSEAI    22 ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG 266
               SCOP domains d1k57d_ D: Class D beta-lactamase                                                                                                                                                                                                                     SCOP domains
               CATH domains 1k57D00 D:22-266 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhhhh..eeeeeee.....eee.hhhhhhhee.hhhhhhhhhhhhhhhh........ee.-----..hhhhhh.eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k57 D  22 ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFK-----RAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG 266
                                    31        41        51        61        71        81        91     | 101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     
                                                                                                91    97

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	d1k57a_	A:
1b	d1k57b_	B:
1c	d1k57c_	C:
1d	d1k57d_	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. (17)

1a	1k57C00	C:22-265
1b	1k57D00	D:22-266
1c	1k57B00	B:21-265
1d	1k57A00	A:22-264

(no "Pfam Domain" information available for 1K57)

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.

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	Cis Peptide Bonds
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	1k57
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1e3u	MAD STRUCTURE OF OXA 10 CLASS D BETA-LACTAMASE
1e4d	STRUCTURE OF OXA 10 BETA-LACTAMASE AT PH 8.3
1k54	OXA10 ACYLATED AT SER67 WITH REACTED 6BETA-(1-HYDROXY-1- METHYLETHYL) PENICILLANIC ACID
1k55	OXA 10 CLASS D BETA-LACTAMASE AT PH 7.5
1k56	OXA 10 CLASS D BETA-LACTAMASE AT PH 6.5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (11, 11)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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