2IO8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   E. COLI BIFUNCTIONAL GLUTATHIONYLSPERMIDINE SYNTHETASE/AMIDASE INCOMPLEX WITH MG2+ AND ADP

Authors :   C. H. Pai, B. Y. Chiang, T. P. Ko, C. C. Chou, C. M. Chong, F. J. Yen, J. K. Coward, A. H. -J. Wang, C. H. Lin

Date :   10 Oct 06 (Deposition) - 12 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Bifunctional Glutathionylspermidine Synthetase/Amidase, Ligase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. H. Pai, B. Y. Chiang, T. P. Ko, C. C. Chou, C. M. Chong, F. J. Yen, S. Chen, J. K. Coward, A. H. -J. Wang, C. H. Lin
Dual Binding Sites For Translocation Catalysis By Escherichia Coli Glutathionylspermidine Synthetase
Embo J. V. 25 5970 2006
PubMed-ID: 17124497 | Reference-DOI: 10.1038/SJ.EMBOJ.7601440
(for further references see the PDB file header)

Molecule 1 - BIFUNCTIONAL GLUTATHIONYLSPERMIDINE SYNTHETASE/AMIDASE
	Chains	:	A, B
	EC Number	:	6.3.1.8, 3.5.1.78
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B (NOVAGEN)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	GLUTATHIONYLSPERMIDINE SYNTHASE, GLUTATHIONYLSPERMIDINE AMIDASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CYS	2	Mod. Amino Acid	CYSTEINE
3	MG	4	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:330 , ASN A:332 , HOH A:4001 , HOH A:4002 , ADP A:5001	BINDING SITE FOR RESIDUE MG A 7001
2	AC2	SOFTWARE	ASP A:318 , GLU A:330 , HOH A:4003 , HOH A:4004 , ADP A:5001	BINDING SITE FOR RESIDUE MG A 7002
3	AC3	SOFTWARE	GLU B:330 , ASN B:332 , HOH B:4005 , HOH B:4006 , ADP B:5002 , MG B:7004	BINDING SITE FOR RESIDUE MG B 7003
4	AC4	SOFTWARE	ASP B:318 , GLU B:330 , HOH B:4007 , HOH B:4008 , ADP B:5002 , MG B:7003	BINDING SITE FOR RESIDUE MG B 7004
5	AC5	SOFTWARE	SER A:337 , CYS A:338 , GLU A:341 , ARG A:598 , LYS A:607 , ILE A:611 , HOH A:3118	BINDING SITE FOR RESIDUE CYS A 5003
6	AC6	SOFTWARE	SER B:337 , CYS B:338 , GLU B:341 , ARG B:598 , LYS B:607 , ILE B:611	BINDING SITE FOR RESIDUE CYS B 5004
7	AC7	SOFTWARE	ASP A:318 , TYR A:329 , GLU A:330 , LYS A:498 , ALA A:531 , LYS A:533 , ARG A:538 , CYS A:539 , GLY A:540 , GLN A:568 , GLN A:569 , TRP A:571 , LEU A:573 , GLN A:582 , LEU A:603 , VAL A:604 , ILE A:605 , HOH A:3027 , HOH A:3117 , HOH A:3152 , HOH A:4001 , HOH A:4002 , HOH A:4003 , HOH A:4004 , MG A:7001 , MG A:7002	BINDING SITE FOR RESIDUE ADP A 5001
8	AC8	SOFTWARE	ASP B:318 , TYR B:329 , GLU B:330 , LYS B:498 , ALA B:531 , LYS B:533 , ARG B:538 , CYS B:539 , GLY B:540 , GLN B:568 , GLN B:569 , TRP B:571 , LEU B:573 , GLN B:582 , LEU B:603 , VAL B:604 , ILE B:605 , HOH B:3100 , HOH B:3101 , HOH B:3854 , HOH B:4005 , HOH B:4006 , HOH B:4007 , HOH B:4008 , MG B:7003 , MG B:7004	BINDING SITE FOR RESIDUE ADP B 5002

(no "SS Bond" information available for 2IO8)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:56	-	Trp A:57
2	Phe A:487	-	Glu A:488
3	Lys B:56	-	Trp B:57
4	Phe B:487	-	Glu B:488

(no "SAP(SNP)/Variant" information available for 2IO8)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHAP	PS50911	CHAP domain profile.	GSP_ECOLI	34-176	2	A:40-176 B:41-176

(no "Exon" information available for 2IO8)

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:598
 aligned with GSP_ECOLI | P0AES0 from UniProtKB/Swiss-Prot  Length:619

    Alignment length:609
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609         
            GSP_ECOLI    10 APFGTLLGYAPGGVAIYSSDYSSLDPQEYEDDAVFRSYIDDEYMGHKWQCVEFARRFLFLNYGVVFTDVGMAWEIFSLRFLREVVNDNILPLQAFPNGSPRAPVAGALLIWDKGGEFKDTGHVAIITQLHGNKVRIAEQNVIHSPLPQGQQWTRELEMVVENGCYTLKDTFDDTTILGWMIQTEDTEYSLPQPEIAGELLKISGARLENKGQFDGKWLDEKDPLQNAYVQANGQVINQDPYHYYTITESAEQELIKATNELHLMYLHATDKVLKDDNLLALFDIPKILWPRLRLSWQRRRHHMITGRMDFCMDERGLKVYEYNADSASCHTEAGLILERWAEQGYKGNGFNPAEGLINELAGAWKHSRARPFVHIMQDKDIEENYHAQFMEQALHQAGFETRILRGLDELGWDAAGQLIDGEGRLVNCVWKTWAWETAFDQIREVSDREFAAVPIRTGHPQNEVRLIDVLLRPEVLVFEPLWTVIPGNKAILPILWSLFPHHRYLLDTDFTVNDELVKTGYAVKPIAGRCGSNIDLVSHHEEVLDKTSGKFAEQKNIYQQLWCLPKVDGKYIQVCTFTVGGNYGGTCLRGDESLVIKKESDIEPLIVVK 618
               SCOP domains d2io8a2 A:10-200 Gluta        thionylspermidine synthase, amidase domain                                                                                                                       d2io8a3 A:201-378,A:497-618 Glutathionylspermidine synthase, synthetase domain                                                                                                    d2io8a1 A:379-496 Glutathionylspermidine synthase, synthetase domain                                                  d2io8a3 A:201-378,A:497-618 Glutathionylspermidine synthase, synthetase domain                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...eeee.....--------hhhh.eeee..eeeee..hhhhhhhhhhhhhhhee.....hhhhhhhh.eeee.hhheeee.eeee...........eeee..hhhhh...eeeeeeee...eeeee................eeeeeeee..eeeee.......eeeeee..............hhhhhh.eeee...............hhhhhhhhhhhh........eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....eeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhhh..eeeeee.....ee.....ee........eeee..hhhhhhhhhhhh---................hhhhhhh....eee.hhhhhh....hhhhhhhhhh........ee...hhhhhhhheeeee.........eee.....eeee.........eeeee.....ee..eeeeeeeeee..eeeeeeeeee.........eee.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------CHAP  PDB: A:40-176 UniProt: 34-176                                                                                                            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2io8 A  10 APFGTLLGYAPGGVAIYSSDYS--------DDAVFRSYIDDEYMGHKWQCVEFARRFLFLNYGVVFTDVGMAWEIFSLRFLREVVNDNILPLQAFPNGSPRAPVAGALLIWDKGGEFKDTGHVAIITQLHGNKVRIAEQNVIHSPLPQGQQWTRELEMVVENGCYTLKDTFDDTTILGWMIQTEDTEYSLPQPEIAGELLKISGARLENKGQFDGKWLDEKDPLQNAYVQANGQVINQDPYHYYTITESAEQELIKATNELHLMYLHATDKVLKDDNLLALFDIPKILWPRLRLSWQRRRHHMITGRMDFCMDERGLKVYEYNADSASCHTEAGLILERWAEQGYKGNGFNPAEGLINELAGAWKHSRARPFVHIMQDKDIEENYHAQFMEQALHQAGFETRILRGLDELGWDAAGQLIDGEGRLVNCVWKTWAWETAFDQIREV---EFAAVPIRTGHPQNEVRLIDVLLRPEVLVFEPLWTVIPGNKAILPILWSLFPHHRYLLDTDFTVNDELVKTGYAVKPIAGRCGSNIDLVSHHEEVLDKTSGKFAEQKNIYQQLWCLPKVDGKYIQVCTFTVGGNYGGTCLRGDESLVIKKESDIEPLIVVK 618
                                    19        29 |       -|       49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449    |  459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609         
                                                31       40                                                                                                                                                                                                                                                                                                                                                                                                                           454 458

Chain B from PDB  Type:PROTEIN  Length:593
 aligned with GSP_ECOLI | P0AES0 from UniProtKB/Swiss-Prot  Length:619

    Alignment length:609
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609         
            GSP_ECOLI    10 APFGTLLGYAPGGVAIYSSDYSSLDPQEYEDDAVFRSYIDDEYMGHKWQCVEFARRFLFLNYGVVFTDVGMAWEIFSLRFLREVVNDNILPLQAFPNGSPRAPVAGALLIWDKGGEFKDTGHVAIITQLHGNKVRIAEQNVIHSPLPQGQQWTRELEMVVENGCYTLKDTFDDTTILGWMIQTEDTEYSLPQPEIAGELLKISGARLENKGQFDGKWLDEKDPLQNAYVQANGQVINQDPYHYYTITESAEQELIKATNELHLMYLHATDKVLKDDNLLALFDIPKILWPRLRLSWQRRRHHMITGRMDFCMDERGLKVYEYNADSASCHTEAGLILERWAEQGYKGNGFNPAEGLINELAGAWKHSRARPFVHIMQDKDIEENYHAQFMEQALHQAGFETRILRGLDELGWDAAGQLIDGEGRLVNCVWKTWAWETAFDQIREVSDREFAAVPIRTGHPQNEVRLIDVLLRPEVLVFEPLWTVIPGNKAILPILWSLFPHHRYLLDTDFTVNDELVKTGYAVKPIAGRCGSNIDLVSHHEEVLDKTSGKFAEQKNIYQQLWCLPKVDGKYIQVCTFTVGGNYGGTCLRGDESLVIKKESDIEPLIVVK 618
               SCOP domains d2io8b2 B:10-200 Gl            utathionylspermidine synthase, amidase domain                                                                                                                   d2io8b3 B:201-378,B:497-618 Glutathionylspermidine synthase, synthetase domain                                                                                                    d2io8b1 B:379-496 Glutathionylspermidine synthase, synthetase domain                                                  d2io8b3 B:201-378,B:497-618 Glutathionylspermidine synthase, synthetase domain                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...eeee..------------hhh.eeee..eeeee..hhhhhhhhhhhhhhhee.....hhhhhhhh.eeee.....eee.eeee...........eeee..hhhhh...eeeeeeee...eeeee................eeeeeeee..eeeee.......eeeeee..............hhhhhh.eeee...............hhhhhhhhhhhh........eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....eeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhhh..eeeeee.....ee.....ee........eeee..hhhhhhhhhhhh----................hhhhhh....eee.hhhhhh....hhhhhhhhhh........ee...hhhhhhhheeeee.........eee.....eeee.........eeeee.....ee..eeeeeeeeee..eeeeeeeeee.........eee.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------CHAP  PDB: B:41-176 UniProt: 34-176                                                                                                            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2io8 B  10 APFGTLLGYAPGGVAIYSS------------DAVFRSYIDDEYMGHKWQCVEFARRFLFLNYGVVFTDVGMAWEIFSLRFLREVVNDNILPLQAFPNGSPRAPVAGALLIWDKGGEFKDTGHVAIITQLHGNKVRIAEQNVIHSPLPQGQQWTRELEMVVENGCYTLKDTFDDTTILGWMIQTEDTEYSLPQPEIAGELLKISGARLENKGQFDGKWLDEKDPLQNAYVQANGQVINQDPYHYYTITESAEQELIKATNELHLMYLHATDKVLKDDNLLALFDIPKILWPRLRLSWQRRRHHMITGRMDFCMDERGLKVYEYNADSASCHTEAGLILERWAEQGYKGNGFNPAEGLINELAGAWKHSRARPFVHIMQDKDIEENYHAQFMEQALHQAGFETRILRGLDELGWDAAGQLIDGEGRLVNCVWKTWAWETAFDQIREV----FAAVPIRTGHPQNEVRLIDVLLRPEVLVFEPLWTVIPGNKAILPILWSLFPHHRYLLDTDFTVNDELVKTGYAVKPIAGRCGSNIDLVSHHEEVLDKTSGKFAEQKNIYQQLWCLPKVDGKYIQVCTFTVGGNYGGTCLRGDESLVIKKESDIEPLIVVK 618
                                    19        |-         - |      49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449    |  459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609         
                                             28           41                                                                                                                                                                                                                                                                                                                                                                                                                          454  459

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 2IO8)

(no "Pfam Domain" information available for 2IO8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GSP_ECOLI | P0AES0)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0008884	glutathionylspermidine amidase activity	Catalysis of the reaction: N1-(gamma-L-glutamyl-L-cysteinyl-glycyl)-spermidine + H2O = gamma-L-glutamyl-L-cysteinyl-glycine + spermidine.
	GO:0008885	glutathionylspermidine synthase activity	Catalysis of the reaction: gamma-L-glutamyl-L-cysteinyl-glycine + spermidine + ATP = N1-(gamma-L-glutamyl-L-cysteinyl-glycyl)-spermidine + ADP + phosphate.
	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.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006749	glutathione metabolic process	The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0008216	spermidine metabolic process	The chemical reactions and pathways involving spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Lys A:56 - Trp A:57	[ RasMol ]
		Lys B:56 - Trp B:57	[ RasMol ]
		Phe A:487 - Glu A:488	[ RasMol ]
		Phe B:487 - Glu B:488	[ RasMol ]

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	2io8
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	3.5.1.78
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	6.3.1.8
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UniProtKB/Swiss-Prot
	GSP_ECOLI \| P0AES0	:	2io7 2io9 2ioa 2iob 3a2y 3a2z 3a30 3o98

2io7	THE SAME PROTEIN COMPLEXED WITH MG2+ AND AMPPNP
2io9	THE SAME PROTEIN COMPLEXED WITH MG2+, GSH AND ADP
2ioa	THE SAME PROTEIN COMPLEXED WITH MG2+, ADP AND PHOSPHINATE INHIBITOR
2iob	THE SAME PROTEIN COMPLEXED WITHOUT LIGANDS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

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