3F7T - JenaLib

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Title :   STRUCTURE OF ACTIVE ISPH SHOWS A NOVEL FOLD WITH A [3FE-4S] CLUSTER IN THE CATALYTIC CENTRE

Authors :   T. Graewert, J. Eppinger, F. Rohdich, A. Bacher, W. Eisenreich, M. Grol

Date :   10 Nov 08 (Deposition) - 07 Jul 09 (Release) - 21 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Pseudo-C3-Symmetry; Unprecedent Fold For Fes-Cluster Proteins, Iron, Iron-Sulfur, Isoprene Biosynthesis, Metal-Binding, Nadp, Oxidoreductase, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Grawert, F. Rohdich, I. Span, A. Bacher, W. Eisenreich, J. Eppinger M. Groll
Structure Of Active Isph Enzyme From Escherichia Coli Provides Mechanistic Insights Into Substrate Reduction.
Angew. Chem. Int. Ed. Engl. V. 48 5756 2009
PubMed-ID: 19569147 | Reference-DOI: 10.1002/ANIE.200900548

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	:	BL21DE3
	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
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	F3S	2	Ligand/Ion	FE3-S4 CLUSTER
2	PO4	8	Ligand/Ion	PHOSPHATE ION
3	POP	2	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
2	PO4	4	Ligand/Ion	PHOSPHATE ION
3	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
2	PO4	4	Ligand/Ion	PHOSPHATE ION
3	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:12 , GLY A:14 , CYS A:96 , THR A:167 , CYS A:197	BINDING SITE FOR RESIDUE F3S A 999
02	AC2	SOFTWARE	VAL A:40 , HIS A:41 , HIS A:74 , HIS A:124 , THR A:168 , ASN A:224 , SER A:225 , SER A:226 , ASN A:227 , SER A:269 , HOH A:467	BINDING SITE FOR RESIDUE POP A 998
03	AC3	SOFTWARE	ASN A:7 , ARG A:9 , PRO A:292	BINDING SITE FOR RESIDUE PO4 A 901
04	AC4	SOFTWARE	ARG A:36 , GLU A:58 , GLN A:59 , ILE A:60 , VAL A:80 , GLU A:83 , HOH A:350	BINDING SITE FOR RESIDUE PO4 A 902
05	AC5	SOFTWARE	ARG A:108 , ARG A:111 , ARG A:112	BINDING SITE FOR RESIDUE PO4 A 904
06	AC6	SOFTWARE	GLN A:252 , GLU A:253	BINDING SITE FOR RESIDUE PO4 A 905
07	AC7	SOFTWARE	CYS B:12 , CYS B:96 , LEU B:98 , THR B:167 , CYS B:197 , HOH B:667	BINDING SITE FOR RESIDUE F3S B 999
08	AC8	SOFTWARE	VAL B:40 , HIS B:41 , HIS B:74 , HIS B:124 , THR B:168 , ASN B:224 , SER B:225 , SER B:226 , ASN B:227 , SER B:269 , HOH B:397 , HOH B:514 , HOH B:667	BINDING SITE FOR RESIDUE POP B 998
09	AC9	SOFTWARE	LYS A:101 , PRO A:191 , PRO B:191 , ARG B:192 , HOH B:321 , HOH B:388 , HOH B:495 , HOH B:529 , HOH B:539	BINDING SITE FOR RESIDUE PO4 B 903
10	BC1	SOFTWARE	ASN B:7 , ARG B:9 , PRO B:292 , HOH B:430 , HOH B:638	BINDING SITE FOR RESIDUE PO4 B 906
11	BC2	SOFTWARE	ARG B:81 , LYS B:85	BINDING SITE FOR RESIDUE PO4 B 907
12	BC3	SOFTWARE	ASN B:157 , HOH B:481	BINDING SITE FOR RESIDUE PO4 B 908

(no "SS Bond" information available for 3F7T)

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 3F7T)

(no "PROSITE Motif" information available for 3F7T)

(no "Exon" information available for 3F7T)

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: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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeee.hhhhh....eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhh........eeee.hhhhhhhh.......eeeee....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh....eee.......eee..hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f7t A   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

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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.hhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh....eee.......eee..hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f7t 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 3F7T)

(no "CATH Domain" information available for 3F7T)

(no "Pfam Domain" information available for 3F7T)

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.

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

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	3f7t
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(no "Related Entries Specified in the PDB File" available for 3F7T)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (12, 12)

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