3KEM - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ISPH:IPP COMPLEX

Authors :   M. Groll, T. Graewert, I. Span, W. Eisenreich, A. Bacher

Date :   26 Oct 09 (Deposition) - 12 Jan 10 (Release) - 04 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Isph, Lytb, Iron Sulfure Protein, Malaria, Tuberculosis, Non- Mevalonic Acid Pathway, Iron, Iron-Sulfur, Isoprene Biosynthesis, Metal-Binding, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Grawert, I. Span, W. Eisenreich, F. Rohdich, J. Eppinger, A. Bacher M. Groll
Probing The Reaction Mechanism Of Isph Protein By X-Ray Structure Analysis.
Proc. Natl. Acad. Sci. Usa V. 107 1077 2010
PubMed-ID: 20080550 | Reference-DOI: 10.1073/PNAS.0913045107

Molecule 1 - 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE
	Chains	:	A, B
	EC Number	:	1.17.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Strain	:	XL1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	B0029, ISPH, JW0027, LYTB, YAAE
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	F3S	2	Ligand/Ion	FE3-S4 CLUSTER
2	IPE	2	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	F3S	2	Ligand/Ion	FE3-S4 CLUSTER
2	IPE	2	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
2	IPE	1	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
2	IPE	1	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:40 , HIS A:41 , ALA A:73 , HIS A:74 , HIS A:124 , THR A:167 , THR A:168 , ASN A:224 , SER A:225 , SER A:226 , ASN A:227 , SER A:269 , HOH A:328 , HOH A:330 , F3S A:997	BINDING SITE FOR RESIDUE IPE A 998
2	AC2	SOFTWARE	CYS A:12 , GLY A:14 , CYS A:96 , LEU A:98 , THR A:167 , CYS A:197 , ALA A:199 , IPE A:998	BINDING SITE FOR RESIDUE F3S A 997
3	AC3	SOFTWARE	VAL B:40 , HIS B:41 , ALA B:73 , HIS B:74 , HIS B:124 , THR B:167 , THR B:168 , ASN B:224 , SER B:225 , SER B:226 , ASN B:227 , SER B:269 , HOH B:350 , HOH B:359 , F3S B:997	BINDING SITE FOR RESIDUE IPE B 998
4	AC4	SOFTWARE	CYS B:12 , GLY B:14 , CYS B:96 , LEU B:98 , THR B:167 , CYS B:197 , THR B:200 , IPE B:998	BINDING SITE FOR RESIDUE F3S B 997

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

Asymmetric Unit

No.	Residues
1	Asn A:7	-	Pro A:8
2	Ala A:31	-	Pro A:32
3	Asn B:7	-	Pro B:8
4	Ala B:31	-	Pro B:32

(no "SAP(SNP)/Variant" information available for 3KEM)

(no "PROSITE Motif" information available for 3KEM)

(no "Exon" information available for 3KEM)

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:309
 aligned with ISPH_ECOLI | P62623 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:309
                                    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         
           ISPH_ECOLI     1 MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELR 309
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeee.hhhhh....eeee.....hhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhh........eeee.hhhhhhhh.......eeeee....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh.....eee............hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kem A   1 MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELR 309
                                    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

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with ISPH_ECOLI | P62623 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:310
                                    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
           ISPH_ECOLI     1 MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELRV 310
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --LYTB-3kemB01 B:3-285                                                                                                                                                                                                                                                                       ------------------------- Pfam domains (1)
           Pfam domains (2) --LYTB-3kemB02 B:3-285                                                                                                                                                                                                                                                                       ------------------------- Pfam domains (2)
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeee.hhhhh....eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhh........eeee.hhhhhhhh.......eeeee....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeeee.hhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh....eee............hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kem B   1 MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELRV 310
                                    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

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 "SCOP Domain" information available for 3KEM)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: LYTB] (4)

Family: LYTB (4)

Escherichia coli (strain K12) (4)

1a	LYTB-3kemB01	B:3-285
1b	LYTB-3kemB02	B:3-285

Asymmetric Unit(hide GO term definitions)

Chain A,B (ISPH_ECOLI | P62623)

molecular function
	GO:0051538	3 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
	GO:0051745	4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity	Catalysis of the reaction: (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+ = isopentenyl diphosphate + NAD(P)+ + H2O. Note that (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate is an alternative name for 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate.
	GO:0042380	hydroxymethylbutenyl pyrophosphate reductase activity	Catalysis of the formation of both isopentenyl pyrophosphate and dimethylallyl pyrophosphate from (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	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:0050992	dimethylallyl diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of dimethylallyl diphosphate.
	GO:0019288	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
	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.
	GO:0016114	terpenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.
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 Unit
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	Ligands, Modified Residues, Ions
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		IPE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
		Ala A:31 - Pro A:32	[ RasMol ]
		Ala B:31 - Pro B:32	[ RasMol ]
		Asn A:7 - Pro A:8	[ RasMol ]
		Asn B:7 - Pro B:8	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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	3kem
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	ISPH_ECOLI \| P62623
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	1.17.1.2
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3dnf	ISPH CLOSED CONFORMATION
3f7t	ISPH OPEN CONFORMATION
3ke8
3ke9
3kef
3kel

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Pfam Domains (1, 2)

Gene Ontology (12, 12)

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Related Entries

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