1P0K - JenaLib

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Title :   IPP:DMAPP ISOMERASE TYPE II APO STRUCTURE

Authors :   S. Steinbacher, J. Kaiser, S. Gerhardt, W. Eisenreich, R. Huber, A. Bac F. Rohdich

Date :   10 Apr 03 (Deposition) - 17 Jun 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)
Biol. Unit 2: A  (4x)
Biol. Unit 3: B  (4x)

Keywords :   Terpene Biosynthesis, Isopentenyl Diphosphate, Dimethylallyl Diphosphate, Isomerase, Flavoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Steinbacher, J. Kaiser, S. Gerhardt, W. Eisenreich, R. Huber, A. Bacher, F. Rohdich
Crystal Structure Of The Type Ii Isopentenyl Diphosphate:Dimethylallyl Diphosphate Isomerase From Bacillus Subtilis
J. Mol. Biol. V. 329 973 2003
PubMed-ID: 12798687 | Reference-DOI: 10.1016/S0022-2836(03)00527-8

Molecule 1 - ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B
Biological Unit 2 (4x)	:	A
Biological Unit 3 (4x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	PO4	8	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	PO4	4	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:258 , GLY A:259 , MET A:279 , ALA A:280 , GLY A:281 , HOH A:1424 , HOH A:1436 , HOH A:1635	BINDING SITE FOR RESIDUE PO4 A 1400
2	AC2	SOFTWARE	GLY B:258 , GLY B:259 , MET B:279 , ALA B:280 , GLY B:281 , HOH B:2401 , HOH B:2440	BINDING SITE FOR RESIDUE PO4 B 2400

(no "SS Bond" information available for 1P0K)

(no "Cis Peptide Bond" information available for 1P0K)

(no "SAP(SNP)/Variant" information available for 1P0K)

(no "PROSITE Motif" information available for 1P0K)

(no "Exon" information available for 1P0K)

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:306
 aligned with IDI2_BACSU | P50740 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:329
                                    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         
           IDI2_BACSU    21 RETGLDDITFVHVSLPDLALEQVDISTKIGELSSSSPIFINAMTGGGGKLTYEINKSLARAASQAGIPLAVGSQMSALKDPSERLSYEIVRKENPNGLIFANLGSEATAAQAKEAVEMIGANALQIHLNVIQEIVMPEGDRSFSGALKRIEQICSRVSVPVIVKEVGFGMSKASAGKLYEAGAAAVDIGGYGGTNFSKIENLRRQRQISFFNSWGISTAASLAEIRSEFPASTMIASGGLQDALDVAKAIALGASCTGMAGHFLKALTDSGEEGLLEEIQLILEELKLIMTVLGARTIADLQKAPLVIKGETHHWLTERGVNTSSYSVR 349
               SCOP domains d1p0ka_ A: Isopentenyl-diphosphate delta-isomerase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1p0kA00 A:21-349 Aldolase class I                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eee........hhhhh...eee..eee...eeee.....hhhhhhhhhhhhhhhhhhhh..ee.........hhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeeeee......--------..hhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhh..eeeee.---------------.hhhhhh....hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...eeehhhhhhhhhhh...hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p0k A  21 RETGLDDITFVHVSLPDLALEQVDISTKIGELSSSSPIFINAMTGGGGKLTYEINKSLARAASQAGIPLAVGSQMSALKDPSERLSYEIVRKENPNGLIFANLGSEATAAQAKEAVEMIGANALQIHLNVIQEI--------FSGALKRIEQICSRVSVPVIVKEVGFGMSKASAGKLYEAGAAAVDIGG---------------RQISFFNSWGISTAASLAEIRSEFPASTMIASGGLQDALDVAKAIALGASCTGMAGHFLKALTDSGEEGLLEEIQLILEELKLIMTVLGARTIADLQKAPLVIKGETHHWLTERGVNTSSYSVR 349
                                    30        40        50        60        70        80        90       100       110       120       130       140       150   |     -  |    170       180       190       200       210         -     | 230       240       250       260       270       280       290       300       310       320       330       340         
                                                                                                                                                               154      163                                            210             226

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with IDI2_BACSU | P50740 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:328
                                    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        
           IDI2_BACSU    22 ETGLDDITFVHVSLPDLALEQVDISTKIGELSSSSPIFINAMTGGGGKLTYEINKSLARAASQAGIPLAVGSQMSALKDPSERLSYEIVRKENPNGLIFANLGSEATAAQAKEAVEMIGANALQIHLNVIQEIVMPEGDRSFSGALKRIEQICSRVSVPVIVKEVGFGMSKASAGKLYEAGAAAVDIGGYGGTNFSKIENLRRQRQISFFNSWGISTAASLAEIRSEFPASTMIASGGLQDALDVAKAIALGASCTGMAGHFLKALTDSGEEGLLEEIQLILEELKLIMTVLGARTIADLQKAPLVIKGETHHWLTERGVNTSSYSVR 349
               SCOP domains d1p0kb_ B: Isopentenyl-diphosphate delta-isomerase                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1p0kB00 B:22-349 Aldolase class I                                                                                                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------F    MN_dh-1p0kB01 B:156-328                                                                                                                                                 --------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------F    MN_dh-1p0kB02 B:156-328                                                                                                                                                 --------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------F    MN_dh-1p0kB03 B:156-328                                                                                                                                                 --------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------F    MN_dh-1p0kB04 B:156-328                                                                                                                                                 --------------------- Pfam domains (4)
         Sec.struct. author ..hhh.eee........hhhhh...eee..eee...eeee.....hhhhhhhhhhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeeeeehhhhhhhh----....hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh..eeee..---------------hhhhhhh....hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...eeehhhhhhhhhhh...hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p0k B  22 ETGLDDITFVHVSLPDLALEQVDISTKIGELSSSSPIFINAMTGGGGKLTYEINKSLARAASQAGIPLAVGSQMSALKDPSERLSYEIVRKENPNGLIFANLGSEATAAQAKEAVEMIGANALQIHLNVIQEIVM----RSFSGALKRIEQICSRVSVPVIVKEVGFGMSKASAGKLYEAGAAAVDIGG---------------RQISFFNSWGISTAASLAEIRSEFPASTMIASGGLQDALDVAKAIALGASCTGMAGHFLKALTDSGEEGLLEEIQLILEELKLIMTVLGARTIADLQKAPLVIKGETHHWLTERGVNTSSYSVR 349
                                    31        41        51        61        71        81        91       101       111       121       131       141       151    |  161       171       181       191       201        |-         -    |  231       241       251       261       271       281       291       301       311       321       331       341        
                                                                                                                                                                156  161                                              210             226

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: FMN-linked oxidoreductases (290)

Family: FMN-linked oxidoreductases (242)

Protein domain: Isopentenyl-diphosphate delta-isomerase (4)

Bacillus subtilis [TaxId: 1423] (2)

1a	d1p0ka_	A:
1b	d1p0kb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Bacillus subtilis. Organism_taxid: 1423. (4)

1a	1p0kA00	A:21-349
1b	1p0kB00	B:22-349

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: FMN_dh (23)

Bacillus subtilis (2)

1a	FMN_dh-1p0kB01	B:156-328
1b	FMN_dh-1p0kB02	B:156-328
1c	FMN_dh-1p0kB03	B:156-328
1d	FMN_dh-1p0kB04	B:156-328

Asymmetric Unit(hide GO term definitions)

Chain A,B (IDI2_BACSU | P50740)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0070402	NADPH binding	Interacting selectively and non-covalently with the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
	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:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0004452	isopentenyl-diphosphate delta-isomerase activity	Catalysis of the reaction: isopentenyl diphosphate = dimethylallyl diphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0008299	isoprenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	IDI2_BACSU \| P50740	:	1p0n

1p0n	1P0N CONTAINS THE SAME PROTEIN COMPLEXED WITH FMN

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

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