3S4X - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE ASN152GLY MUTANT OF P99 BETA-LACTAMASE

Authors :   J. F. Ruble, R. A. Powers

Date :   20 May 11 (Deposition) - 01 Aug 12 (Release) - 23 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

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

Reference :   J. F. Ruble, S. T. Lefurgy, V. W. Cornish, R. A. Powers
Structural Analysis Of The Asn152Gly Mutant Of P99 Cephalosporinase.
Acta Crystallogr. , Sect. D V. 68 1189 2012
PubMed-ID: 22948919 | Reference-DOI: 10.1107/S0907444912024080

Molecule 1 - BETA-LACTAMASE
	Chains	:	A
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET26
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	AMPC
	Mutation	:	YES
	Organism Scientific	:	ENTEROBACTER CLOACAE
	Organism Taxid	:	550
	Strain	:	P99
	Synonym	:	CEPHALOSPORINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 7)

No.	Name	Count	Type	Full Name
1	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 7)

No.	Name	Count	Type	Full Name
1	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 14)

No.	Name	Count	Type	Full Name
1	SO4	14	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:365 , HIS A:367 , HOH A:593	BINDING SITE FOR RESIDUE SO4 A 368
2	AC2	SOFTWARE	ARG A:261 , GLY A:263 , TRP A:276 , PRO A:277 , LYS A:332 , HOH A:499 , HOH A:558	BINDING SITE FOR RESIDUE SO4 A 369
3	AC3	SOFTWARE	VAL A:211 , SER A:212 , GLY A:320 , HIS A:364 , HIS A:365 , HIS A:366 , HOH A:503	BINDING SITE FOR RESIDUE SO4 A 370
4	AC4	SOFTWARE	LYS A:99 , LYS A:183	BINDING SITE FOR RESIDUE SO4 A 371
5	AC5	SOFTWARE	PRO A:18 , LYS A:21 , ARG A:133 , ASN A:137 , HOH A:409 , HOH A:477	BINDING SITE FOR RESIDUE SO4 A 372
6	AC6	SOFTWARE	SER A:64 , TYR A:150 , LYS A:315 , THR A:316 , GLY A:317 , SER A:318 , ASN A:346 , HIS A:367 , HOH A:420 , HOH A:562 , HOH A:594	BINDING SITE FOR RESIDUE SO4 A 373
7	AC7	SOFTWARE	SER A:4 , GLU A:5 , HOH A:509	BINDING SITE FOR RESIDUE SO4 A 374

(no "SS Bond" information available for 3S4X)

Asymmetric Unit

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

Asymmetric Unit (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AMPC_ENTCL_003 *	T	21	A	AMPC_ENTCL	---	---	A	T	1	A
2	UniProt	VAR_AMPC_ENTCL_004 *	I	36	V	AMPC_ENTCL	---	---	A	V	16	V
3	UniProt	VAR_AMPC_ENTCL_005 *	P	58	S	AMPC_ENTCL	---	---	A	P	38	S
4	UniProt	VAR_AMPC_ENTCL_006 *	A	108	P	AMPC_ENTCL	---	---	A	P	88	P
5	UniProt	VAR_AMPC_ENTCL_007 *	L	152	V	AMPC_ENTCL	---	---	A	L	132	V
6	UniProt	VAR_AMPC_ENTCL_008 *	N	262	K	AMPC_ENTCL	---	---	A	N	242	K
7	UniProt	VAR_AMPC_ENTCL_009 *	A	319	V	AMPC_ENTCL	---	---	A	V	299	V
8	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 1 (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AMPC_ENTCL_003 *	T	21	A	AMPC_ENTCL	---	---	A	T	1	A
2	UniProt	VAR_AMPC_ENTCL_004 *	I	36	V	AMPC_ENTCL	---	---	A	V	16	V
3	UniProt	VAR_AMPC_ENTCL_005 *	P	58	S	AMPC_ENTCL	---	---	A	P	38	S
4	UniProt	VAR_AMPC_ENTCL_006 *	A	108	P	AMPC_ENTCL	---	---	A	P	88	P
5	UniProt	VAR_AMPC_ENTCL_007 *	L	152	V	AMPC_ENTCL	---	---	A	L	132	V
6	UniProt	VAR_AMPC_ENTCL_008 *	N	262	K	AMPC_ENTCL	---	---	A	N	242	K
7	UniProt	VAR_AMPC_ENTCL_009 *	A	319	V	AMPC_ENTCL	---	---	A	V	299	V
8	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 (8, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AMPC_ENTCL_003 *	T	21	A	AMPC_ENTCL	---	---	A	T	1	A
2	UniProt	VAR_AMPC_ENTCL_004 *	I	36	V	AMPC_ENTCL	---	---	A	V	16	V
3	UniProt	VAR_AMPC_ENTCL_005 *	P	58	S	AMPC_ENTCL	---	---	A	P	38	S
4	UniProt	VAR_AMPC_ENTCL_006 *	A	108	P	AMPC_ENTCL	---	---	A	P	88	P
5	UniProt	VAR_AMPC_ENTCL_007 *	L	152	V	AMPC_ENTCL	---	---	A	L	132	V
6	UniProt	VAR_AMPC_ENTCL_008 *	N	262	K	AMPC_ENTCL	---	---	A	N	242	K
7	UniProt	VAR_AMPC_ENTCL_009 *	A	319	V	AMPC_ENTCL	---	---	A	V	299	V
8	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)

Asymmetric Unit (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 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, 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

(no "Exon" information available for 3S4X)

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:367
 aligned with AMPC_ENTCL | P05364 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:367
                                                                                                                                                                                                                                                                                                                                                                                                  381      
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380|      
           AMPC_ENTCL    21 TPVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDAVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ------   -
               SCOP domains d3s4xa_ A: AMPC beta-Lactamase, class C                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhh.....hhhhh..hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhh.....hhhhhhhhhh........ee...hhhhhhhh..eee..eee......hhhhhh..eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhhhhhhhhhh..ee.eeeeeee.....eeeeeeee....eeeeeee....eeeeeee....hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) A--------------V---------------------S-------------------------------------------------P-------------------------------------------V-------------------------------------------------------------------------------------------------------------K--------------------------------------------------------V------------------------------------------K------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------BETA_LAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s4x A   1 TPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYAGASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQHHHHHH 367
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360

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 '\|'

(no "CATH Domain" information available for 3S4X)

(no "Pfam Domain" information available for 3S4X)

Asymmetric Unit(hide GO term definitions)

Chain A (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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	AMPC_ENTCL \| P05364	:	1bls 1gce 1rgz 1xx2 1y54 2q9m 2q9n 4xux 5hai

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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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