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Title :   CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE PHOSPHOTRANSFERASE TYPE IIIA ADP COMPLEX

Authors :   D. L. Burk, W. C. Hon, A. K. -W. Leung, A. M. Berghuis

Date :   17 May 01 (Deposition) - 08 Aug 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B

Keywords :   Antibiotic Resistance, Kinase, Atp-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. L. Burk, W. C. Hon, A. K. Leung, A. M. Berghuis
Structural Analyses Of Nucleotide Binding To An Aminoglycoside Phosphotransferase.
Biochemistry V. 40 8756 2001
PubMed-ID: 11467935 | Reference-DOI: 10.1021/BI010504P
(for further references see the PDB file header)

Molecule 1 - AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.7.1.95
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PPCRG6
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ENTEROCOCCUS FAECALIS
	Organism Taxid	:	1351
	Synonym	:	APH(3')III

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	4	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:195 , ASP A:208 , MG A:302 , ADP A:303 , HOH A:438 , HOH A:482	BINDING SITE FOR RESIDUE MG A 301
2	AC2	SOFTWARE	ASP A:208 , MG A:301 , ADP A:303 , HOH A:423 , HOH A:479 , HOH A:483	BINDING SITE FOR RESIDUE MG A 302
3	AC3	SOFTWARE	ASN B:195 , ASP B:208 , ADP B:304 , HOH B:402 , HOH B:467	BINDING SITE FOR RESIDUE MG B 301
4	AC4	SOFTWARE	ASP B:208 , ADP B:304 , HOH B:451 , HOH B:452 , HOH B:465	BINDING SITE FOR RESIDUE MG B 302
5	AC5	SOFTWARE	ASP A:22 , GLU A:24 , SER A:27 , VAL A:31 , TYR A:42 , LYS A:44 , MET A:90 , SER A:91 , GLU A:92 , ALA A:93 , LEU A:97 , SER A:194 , ASN A:195 , PHE A:197 , ILE A:207 , ASP A:208 , MG A:301 , MG A:302 , HOH A:413 , HOH A:423 , HOH A:438 , HOH A:483 , HOH A:491 , HOH A:542	BINDING SITE FOR RESIDUE ADP A 303
6	AC6	SOFTWARE	ASP B:22 , GLU B:24 , SER B:27 , VAL B:31 , TYR B:42 , LYS B:44 , MET B:90 , SER B:91 , GLU B:92 , ALA B:93 , LEU B:97 , SER B:194 , ASN B:195 , PHE B:197 , ILE B:207 , ASP B:208 , MG B:301 , MG B:302 , HOH B:402 , HOH B:439 , HOH B:451 , HOH B:459 , HOH B:465 , HOH B:467 , HOH B:492 , HOH B:520	BINDING SITE FOR RESIDUE ADP B 304

Asymmetric/Biological Unit

No.	Residues
1	A:19	-	B:156
2	A:156	-	B:19

(no "Cis Peptide Bond" information available for 1J7L)

(no "SAP(SNP)/Variant" information available for 1J7L)

(no "PROSITE Motif" information available for 1J7L)

(no "Exon" information available for 1J7L)

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
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Chain A from PDB  Type:PROTEIN  Length:263
 aligned with KKA3_ENTFL | P0A3Y5 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:263
                                    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   
           KKA3_ENTFL     2 AKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDWEKIKYYILLDELF 264
               SCOP domains d1j7la_ A: Type IIIa 3',5-aminoglycoside phosphotransferase                                                                                                                                                                                                             SCOP domains
               CATH domains 1j7lA01 A:2-91 Phosphorylase Kinase; domain 1                                             1j7lA02 A:92-264  [code=3.90.1200.10, no name defined]                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..eeee........eeeeee....eeeeeeehhhhh....hhhhhhhhhhhhh.......eeeeeee..eeeeeee....eehhhhh....hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.....hhhhhh......hhhhhhhhhhhh.....eeee........eeee..eeeee......eeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j7l A   2 AKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDWEKIKYYILLDELF 264
                                    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

Chain B from PDB  Type:PROTEIN  Length:263
 aligned with KKA3_ENTFL | P0A3Y5 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:263
                                    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   
           KKA3_ENTFL     2 AKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDWEKIKYYILLDELF 264
               SCOP domains d1j7lb_ B: Type IIIa 3',5-aminoglycoside phosphotransferase                                                                                                                                                                                                             SCOP domains
               CATH domains 1j7lB01 B:2-91 Phosphorylase Kinase; domain 1                                             1j7lB02 B:92-264  [code=3.90.1200.10, no name defined]                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..eeee........eeeeee....eeeeeeehhhhh....hhhhhhhhhhhh........eeeeeee..eeeeeee....eehhhhh....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh......hhhhh......hhhhhhhhhhhh.....eeee........eeee..eeeee......eeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j7l B   2 AKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDWEKIKYYILLDELF 264
                                    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

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Protein kinase-like (PK-like) (2589)

Superfamily: Protein kinase-like (PK-like) (2589)

Family: APH phosphotransferases (17)

Protein domain: Type IIIa 3',5-aminoglycoside phosphotransferase (8)

Enterococcus faecalis [TaxId: 1351] (8)

1a	d1j7la_	A:
1b	d1j7lb_	B:

(no "Pfam Domain" information available for 1J7L)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (KKA3_ENTFL | P0A3Y5)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008910	kanamycin kinase activity	Catalysis of the reaction: ATP + kanamycin = ADP + 2 H(+) + kanamycin 3'-phosphate.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016773	phosphotransferase activity, alcohol group as acceptor	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	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.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 1j7l)

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1j7i	1J7I CONTAINS THE APOENZYME FORM OF THIS PROTEIN
1j7u	1J7U CONTAINS THE THE SAME ENZYME COMPLEXED WITH AMPPNP

Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (2, 2)

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