1BLS - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTALLOGRAPHIC STRUCTURE OF A PHOSPHONATE DERIVATIVE OF THE ENTEROBACTER CLOACAE P99 CEPHALOSPORINASE: MECHANISTIC INTERPRETATION OF A BETA-LACTAMASE TRANSITION STATE ANALOG

Authors :   J. R. Knox, P. C. Moews, E. Lobkovsky

Date :   17 Dec 93 (Deposition) - 08 May 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Hydrolase (Acting In Cyclic Amides) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Lobkovsky, E. M. Billings, P. C. Moews, J. Rahil, R. F. Pratt, J. R. Knox
Crystallographic Structure Of A Phosphonate Derivative Of The Enterobacter Cloacae P99 Cephalosporinase: Mechanistic Interpretation Of A Beta-Lactamase Transition-State Analog.
Biochemistry V. 33 6762 1994
PubMed-ID: 8204611 | Reference-DOI: 10.1021/BI00188A004
(for further references see the PDB file header)

Molecule 1 - BETA-LACTAMASE
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Organism Scientific	:	ENTEROBACTER CLOACAE
	Organism Taxid	:	550

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	IPP	2	Ligand/Ion	(P-IODOPHENYLACETYLAMINO)METHYLPHOSPHINIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	IPP	1	Ligand/Ion	(P-IODOPHENYLACETYLAMINO)METHYLPHOSPHINIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	IPP	1	Ligand/Ion	(P-IODOPHENYLACETYLAMINO)METHYLPHOSPHINIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:64 , GLN A:120 , TYR A:150 , ASN A:152 , TYR A:221 , GLY A:317 , SER A:318 , GLY A:320 , HOH A:563	BINDING SITE FOR RESIDUE IPP A 362
2	AC2	SOFTWARE	SER B:64 , GLN B:120 , TYR B:150 , ASN B:152 , TYR B:221 , GLY B:317 , SER B:318 , HOH B:480 , HOH B:657	BINDING SITE FOR RESIDUE IPP B 362

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

Asymmetric Unit

No.	Residues
1	Trp A:276	-	Pro A:277
2	Asn A:302	-	Pro A:303
3	Trp B:276	-	Pro B:277
4	Asn B:302	-	Pro B:303

Asymmetric Unit (7, 14)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AMPC_ENTCL_004 *	I	36	V	AMPC_ENTCL	---	---	A/B	I	16	V
2	UniProt	VAR_AMPC_ENTCL_005 *	P	58	S	AMPC_ENTCL	---	---	A/B	P	38	S
3	UniProt	VAR_AMPC_ENTCL_006 *	A	108	P	AMPC_ENTCL	---	---	A/B	A	88	P
4	UniProt	VAR_AMPC_ENTCL_007 *	L	152	V	AMPC_ENTCL	---	---	A/B	L	132	V
5	UniProt	VAR_AMPC_ENTCL_008 *	N	262	K	AMPC_ENTCL	---	---	A/B	N	242	K
6	UniProt	VAR_AMPC_ENTCL_009 *	A	319	V	AMPC_ENTCL	---	---	A/B	A	299	V
7	UniProt	VAR_AMPC_ENTCL_010 *	T	362	K	AMPC_ENTCL	---	---	A/B	T	342	K
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AMPC_ENTCL_004 *	I	36	V	AMPC_ENTCL	---	---	A	I	16	V
2	UniProt	VAR_AMPC_ENTCL_005 *	P	58	S	AMPC_ENTCL	---	---	A	P	38	S
3	UniProt	VAR_AMPC_ENTCL_006 *	A	108	P	AMPC_ENTCL	---	---	A	A	88	P
4	UniProt	VAR_AMPC_ENTCL_007 *	L	152	V	AMPC_ENTCL	---	---	A	L	132	V
5	UniProt	VAR_AMPC_ENTCL_008 *	N	262	K	AMPC_ENTCL	---	---	A	N	242	K
6	UniProt	VAR_AMPC_ENTCL_009 *	A	319	V	AMPC_ENTCL	---	---	A	A	299	V
7	UniProt	VAR_AMPC_ENTCL_010 *	T	362	K	AMPC_ENTCL	---	---	A	T	342	K
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AMPC_ENTCL_004 *	I	36	V	AMPC_ENTCL	---	---	B	I	16	V
2	UniProt	VAR_AMPC_ENTCL_005 *	P	58	S	AMPC_ENTCL	---	---	B	P	38	S
3	UniProt	VAR_AMPC_ENTCL_006 *	A	108	P	AMPC_ENTCL	---	---	B	A	88	P
4	UniProt	VAR_AMPC_ENTCL_007 *	L	152	V	AMPC_ENTCL	---	---	B	L	132	V
5	UniProt	VAR_AMPC_ENTCL_008 *	N	262	K	AMPC_ENTCL	---	---	B	N	242	K
6	UniProt	VAR_AMPC_ENTCL_009 *	A	319	V	AMPC_ENTCL	---	---	B	A	299	V
7	UniProt	VAR_AMPC_ENTCL_010 *	T	362	K	AMPC_ENTCL	---	---	B	T	342	K
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_C	PS00336	Beta-lactamase class-C active site.	AMPC_ENTCL	80-87	2	A:60-67 B:60-67

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_C	PS00336	Beta-lactamase class-C active site.	AMPC_ENTCL	80-87	1	A:60-67 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_C	PS00336	Beta-lactamase class-C active site.	AMPC_ENTCL	80-87	1	- B:60-67

(no "Exon" information available for 1BLS)

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:359
 aligned with AMPC_ENTCL | P05364 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:359
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371         
           AMPC_ENTCL    22 PVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDAVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEAL 380
               SCOP domains d1blsa_ A: AMPC beta-Lactamase, class C                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1blsA00 A:2-360 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeeeeee..........eeee.hhhhhhhhhhhhhhhhh.........hhhh......hhh....hhhhhh................hhhhhhhhhh..............hhhhhhhhhhh.......hhhhhhhhhhh.....eeee...........................hhhh...eeehhhhhhhhhhhh.......hhhhhhhhhh..eeeee..eee....eeee....hhhhhhh..hhhh...eeeeeeeeee.....eeeeeeee....eeeeeee....eeeeeee.....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------V---------------------S-------------------------------------------------P-------------------------------------------V-------------------------------------------------------------------------------------------------------------K--------------------------------------------------------V------------------------------------------K------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------BETA_LAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bls A   2 PVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDAVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEAL 360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351

Chain B from PDB  Type:PROTEIN  Length:359
 aligned with AMPC_ENTCL | P05364 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:359
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371         
           AMPC_ENTCL    22 PVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDAVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEAL 380
               SCOP domains d1blsb_ B: AMPC beta-Lactamase, class C                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1blsB00 B:2-360 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeeeeee..........eeee.hhhhhhhhhhhhhhhhh.........hhhh......hhh....hhhhhh................hhhhhhhhhh..............hhhhhhhhhhh.......hhhhhhhhhhh.....eeee...........................hhhh...eeehhhhhhhhhhhh.......hhhhhhhhhh..eeeee..eee....eeee....hhhhhhh..hhhh...eeeeeeeeee.....eeeeeeee....eeeeeee....eeeeeee.....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------V---------------------S-------------------------------------------------P-------------------------------------------V-------------------------------------------------------------------------------------------------------------K--------------------------------------------------------V------------------------------------------K------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------BETA_LAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bls B   2 PVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDAVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEAL 360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351

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(

)

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)

Enterobacter cloacae. Organism_taxid: 550 (2)

1a	1blsA00	A:2-360
1b	1blsB00	B:2-360

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (AMPC_ENTCL | P05364)

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: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:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	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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		Trp A:276 - Pro A:277	[ RasMol ]
		Trp B:276 - Pro B:277	[ RasMol ]

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	1bls
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	AMPC_ENTCL \| P05364	:	1gce 1rgz 1xx2 1y54 2q9m 2q9n 3s4x 4xux 5hai

(no "Related Entries Specified in the PDB File" available for 1BLS)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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