1RGY - JenaLib

Title :   CITROBACTER FREUNDII GN346 CLASS C BETA-LACTAMASE COMPLEXED WITH TRANSITION-STATE ANALOG OF CEFOTAXIME

Authors :   M. Nukaga, S. Kumar, K. Nukaga, R. F. Pratt, J. R. Knox

Date :   13 Nov 03 (Deposition) - 06 Apr 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.52

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Cephalosporinase, Enzyme Inhibition, Phosphonate, Beta-Lactam Antibiotics, Drug Design (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Nukaga, S. Kumar, K. Nukaga, R. F. Pratt, J. R. Knox
Hydrolysis Of Third-Generation Cephalosporins By Class C Beta-Lactamases. Structures Of A Transition State Analog Of Cefotoxamine In Wild-Type And Extended Spectrum Enzymes.
J. Biol. Chem. V. 279 9344 2004
PubMed-ID: 14660590 | Reference-DOI: 10.1074/JBC.M312356200
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (9, 9)

Asymmetric/Biological Unit (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AMPC_CITFR_001 *	R	97	A	AMPC_CITFR	---	---	A	A	77	A
2	UniProt	VAR_AMPC_CITFR_002 *	G	143	D	AMPC_CITFR	---	---	A	D	123	D
3	UniProt	VAR_AMPC_CITFR_003 *	V	145	I	AMPC_CITFR	---	---	A	I	125	I
4	UniProt	VAR_AMPC_CITFR_004 *	E	150	A	AMPC_CITFR	---	---	A	A	130	A
5	UniProt	VAR_AMPC_CITFR_005 *	S	185	P	AMPC_CITFR	---	---	A	P	165	P
6	UniProt	VAR_AMPC_CITFR_006 *	L	224	R	AMPC_CITFR	---	---	A	R	204	R
7	UniProt	VAR_AMPC_CITFR_007 *	V	243	L	AMPC_CITFR	---	---	A	V	223	L
8	UniProt	VAR_AMPC_CITFR_008 *	A	325	V	AMPC_CITFR	---	---	A	V	305	V
9	UniProt	VAR_AMPC_CITFR_009 *	A	368	V	AMPC_CITFR	---	---	A	V	348	V
	* ID not provided by source

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

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:360
 aligned with AMPC_CITFR | P05193 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:360
                                    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       381
           AMPC_CITFR    22 AKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDRIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPGDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKSSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYLEGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ 381
               SCOP domains d1rgya_ A: AMPC beta-Lactamase, class C                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1rgyA00 A:2-361 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ----------Beta-lactamase-1rgyA01 A:12-361                                                                                                                                                                                                                                                                                                                                Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhhh....hhhhh..hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhh.....hhhhhhhhhh........ee...hhhhhhhh..eee..eee......hhhhhh..eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhhhhhhhhhh..ee.eeeeeee.....eeeeeeee....eeeeeeehhhheeeeeee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------A---------------------------------------------D-I----A----------------------------------P--------------------------------------R------------------L---------------------------------------------------------------------------------V------------------------------------------V------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------BETA_LAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rgy A   2 AKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPVPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ 361
                                    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       361

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	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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (AMPC_CITFR | P05193)

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).

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