1XX2 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   REFINEMENT OF P99 BETA-LACTAMASE FROM ENTEROBACTER CLOACAE

Authors :   J. R. Knox, T. Sun

Date :   03 Nov 04 (Deposition) - 23 Nov 04 (Release) - 12 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.88

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

Keywords :   Class C Beta-Lactamase, Cephalosporinase, Penicillinase, Ampc, Enterobacter Cloacae, Antibiotic Resistance, Serine Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Knox, T. Sun
Refinement Of P99 Beta-Lactamase From Enterobacter Cloacae
To Be Published
PubMed: search

Molecule 1 - BETA-LACTAMASE
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Organism Scientific	:	ENTEROBACTER CLOACAE
	Organism Taxid	:	550
	Strain	:	P99
	Synonym	:	CEPHALOSPORINASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1XX2)

(no "Site" information available for 1XX2)

(no "SS Bond" information available for 1XX2)

Asymmetric Unit

No.	Residues
1	Trp A:276	-	Pro A:277
2	Asn A:302	-	Pro A:303
3	Trp B:1276	-	Pro B:1277
4	Asn B:1302	-	Pro B:1303

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 1016	V
2	UniProt	VAR_AMPC_ENTCL_005 *	P	58	S	AMPC_ENTCL	---	---	A B	P	38 1038	S
3	UniProt	VAR_AMPC_ENTCL_006 *	A	108	P	AMPC_ENTCL	---	---	A B	A	88 1088	P
4	UniProt	VAR_AMPC_ENTCL_007 *	L	152	V	AMPC_ENTCL	---	---	A B	L	132 1132	V
5	UniProt	VAR_AMPC_ENTCL_008 *	N	262	K	AMPC_ENTCL	---	---	A B	N	242 1242	K
6	UniProt	VAR_AMPC_ENTCL_009 *	A	319	V	AMPC_ENTCL	---	---	A B	A	299 1299	V
7	UniProt	VAR_AMPC_ENTCL_010 *	T	362	K	AMPC_ENTCL	---	---	A B	T	342 1342	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 A	I	16 1016	V
2	UniProt	VAR_AMPC_ENTCL_005 *	P	58	S	AMPC_ENTCL	---	---	A A	P	38 1038	S
3	UniProt	VAR_AMPC_ENTCL_006 *	A	108	P	AMPC_ENTCL	---	---	A A	A	88 1088	P
4	UniProt	VAR_AMPC_ENTCL_007 *	L	152	V	AMPC_ENTCL	---	---	A A	L	132 1132	V
5	UniProt	VAR_AMPC_ENTCL_008 *	N	262	K	AMPC_ENTCL	---	---	A A	N	242 1242	K
6	UniProt	VAR_AMPC_ENTCL_009 *	A	319	V	AMPC_ENTCL	---	---	A A	A	299 1299	V
7	UniProt	VAR_AMPC_ENTCL_010 *	T	362	K	AMPC_ENTCL	---	---	A A	T	342 1342	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	---	---	A B	I	16 1016	V
2	UniProt	VAR_AMPC_ENTCL_005 *	P	58	S	AMPC_ENTCL	---	---	A B	P	38 1038	S
3	UniProt	VAR_AMPC_ENTCL_006 *	A	108	P	AMPC_ENTCL	---	---	A B	A	88 1088	P
4	UniProt	VAR_AMPC_ENTCL_007 *	L	152	V	AMPC_ENTCL	---	---	A B	L	132 1132	V
5	UniProt	VAR_AMPC_ENTCL_008 *	N	262	K	AMPC_ENTCL	---	---	A B	N	242 1242	K
6	UniProt	VAR_AMPC_ENTCL_009 *	A	319	V	AMPC_ENTCL	---	---	A B	A	299 1299	V
7	UniProt	VAR_AMPC_ENTCL_010 *	T	362	K	AMPC_ENTCL	---	---	A B	T	342 1342	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:1060-1067

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:1060-1067

(no "Exon" information available for 1XX2)

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 d1xx2a_ A: AMPC beta-Lactamase, class C                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1xx2A00 A:2-360 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhhh....hhhhh..hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhhh.hhhhhhhhhh........ee...hhhhhhhh..eee..eee......hhhhhh..eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhhhhhhhhhh..ee.eeeeeee.....eeeeeeee....eeeeeee....eeeeeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------BETA_LAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xx2 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 d1xx2b_ B: AMPC beta-Lactamase, class C                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1xx2B00 B:1002-1360 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ----------Beta-lactamase-1xx2B01 B:1012-1360                                                                                                                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) ----------Beta-lactamase-1xx2B02 B:1012-1360                                                                                                                                                                                                                                                                                                                            Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh..eeeeeee....eeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhh.....hhhhh..hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhhh.hhhhhhhhhh.............hhhhhhhh..eee..eee......hhhhhh..eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhhhhhhhhhh..ee.eeeeeee.....eeeeeeee....eeeeeee....eeeeeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------V---------------------S-------------------------------------------------P-------------------------------------------V-------------------------------------------------------------------------------------------------------------K--------------------------------------------------------V------------------------------------------K------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------BETA_LAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xx2 B 1002 PVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDAVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEAL 1360
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351

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. Strain: p99 (1)

1a	1xx2A00	A:2-360
1b	1xx2B00	B:1002-1360

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta-lactamase (210)

Family: Beta-lactamase (79)

Enterobacter cloacae (8)

1a	Beta-lactamase-1xx2B01	B:1012-1360
1b	Beta-lactamase-1xx2B02	B:1012-1360

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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	Ligands, Modified Residues, Ions
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	Sites
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	Cis Peptide Bonds
		Asn A:302 - Pro A:303	[ RasMol ]
		Asn B:1302 - Pro B:1303	[ RasMol ]
		Trp A:276 - Pro A:277	[ RasMol ]
		Trp B:1276 - Pro B:1277	[ RasMol ]

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	3.5.2.6
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	AMPC_ENTCL \| P05364	:	1bls 1gce 1rgz 1y54 2q9m 2q9n 3s4x 4xux 5hai

1bls	CRYSTALLOGRAPHIC STRUCTURE OF A PHOSPHONATE DERIVATIVE OF THE ENTEROBACTER CLOACAE P99 CEPHALOSPORINASE: MECHANISTIC INTERPRETATION OF A BETA-LACTAMASE TRANSITION STATE ANALOG
2blt	EVOLUTION OF AN ENZYME ACTIVITY: STRUCTURE AT 2 ANGSTROMS RESOLUTION OF CEPHALOSPORINASE FROM THE AMPC GENE OF ENTEROBACTER CLOACAE P99 AND COMPARISON WITH A CLASS A PENICILLINASE. PROC.NATL.ACAD.SCI., V.90, 11257-1993. PDB ENTRY 2BLT HAS BEEN OBSOLETED BY THIS ENTRY, 1XX2.

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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SAPs(SNPs)/Variants (7, 14)

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Exons (0, 0)

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