3ERN - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CLYCODIPHOSPHATE SYNTHASE COMPLEXED WITH ARACMP

Authors :   W. N. Hunter, N. L. Ramsden, L. A. Kemp

Date :   02 Oct 08 (Deposition) - 25 Aug 09 (Release) - 25 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D,E,F  (1x)

Keywords :   Mecdp-Synthase, Isoprene Biosynthesis, Lyase, Magnesium, Manganese, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. L. Ramsden, L. Buetow, A. Dawson, L. A. Kemp, V. Ulaganathan, R. Brenk, G. Klebe, W. N. Hunter
A Structure-Based Approach To Ligand Discovery For 2C-Methyl-D-Erythritol-2, 4-Cyclodiphosphate Synthase: A Target For Antimicrobial Therapy
J. Med. Chem. V. 52 2531 2009
PubMed-ID: 19320487 | Reference-DOI: 10.1021/JM801475N
(for further references see the PDB file header)

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	4.6.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ISPF
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	MECPS, MECDP-SYNTHASE

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 13)

No.	Name	Count	Type	Full Name
1	CAR	5	Mod. Residue	CYTOSINE ARABINOSE-5'-PHOSPHATE
2	GPP	2	Ligand/Ion	GERANYL DIPHOSPHATE
3	SO4	2	Ligand/Ion	SULFATE ION
4	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	CAR	3	Mod. Residue	CYTOSINE ARABINOSE-5'-PHOSPHATE
2	GPP	1	Ligand/Ion	GERANYL DIPHOSPHATE
3	SO4	1	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	CAR	2	Mod. Residue	CYTOSINE ARABINOSE-5'-PHOSPHATE
2	GPP	1	Ligand/Ion	GERANYL DIPHOSPHATE
3	SO4	1	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:8 , HIS A:10 , HIS A:42	BINDING SITE FOR RESIDUE ZN A 800
02	AC2	SOFTWARE	ALA A:100 , PRO A:103 , LYS A:104 , MET A:105 , LEU A:106 , ALA A:131 , THR A:132 , THR A:133 , HOH A:927 , ASP C:56 , GLY C:58 , HOH C:929	BINDING SITE FOR RESIDUE CAR A 900
03	AC3	SOFTWARE	ASP A:56 , ALA B:100 , PRO B:103 , LYS B:104 , MET B:105 , LEU B:106 , ALA B:131 , THR B:132 , THR B:133 , HOH B:920 , HOH B:932 , HOH B:939	BINDING SITE FOR RESIDUE CAR B 900
04	AC4	SOFTWARE	ASP B:8 , HIS B:10 , HIS B:42 , SO4 B:801	BINDING SITE FOR RESIDUE ZN B 800
05	AC5	SOFTWARE	HIS B:10 , HIS B:34 , SER B:35 , ZN B:800 , HOH B:917 , HOH B:940	BINDING SITE FOR RESIDUE SO4 B 801
06	AC6	SOFTWARE	GLY A:138 , PHE A:139 , ARG A:142 , THR B:134 , GLY B:138 , PHE B:139 , THR B:140 , ARG B:142 , GLY C:138 , PHE C:139 , ARG C:142 , GLU C:149	BINDING SITE FOR RESIDUE GPP B 901
07	AC7	SOFTWARE	ASP B:56 , ALA C:100 , PRO C:103 , LYS C:104 , MET C:105 , LEU C:106 , ALA C:131 , THR C:132 , THR C:133 , HOH C:904	BINDING SITE FOR RESIDUE CAR C 900
08	AC8	SOFTWARE	ASP D:8 , HIS D:10 , HIS D:42	BINDING SITE FOR RESIDUE ZN D 800
09	AC9	SOFTWARE	ALA D:100 , PRO D:103 , LYS D:104 , MET D:105 , LEU D:106 , ALA D:131 , THR D:132 , THR D:133 , HOH D:903 , HOH D:937 , ASP F:56 , GLY F:58	BINDING SITE FOR RESIDUE CAR D 900
10	BC1	SOFTWARE	ASP D:56 , GLY D:58 , ALA E:100 , PRO E:103 , LYS E:104 , MET E:105 , LEU E:106 , ALA E:131 , THR E:132 , THR E:133 , HOH E:902 , HOH E:916	BINDING SITE FOR RESIDUE CAR E 900
11	BC2	SOFTWARE	ASP E:8 , HIS E:10 , HIS E:42 , SO4 E:801 , HOH E:943	BINDING SITE FOR RESIDUE ZN E 800
12	BC3	SOFTWARE	HIS E:10 , ALA E:33 , HIS E:34 , SER E:35 , HIS E:42 , ZN E:800 , HOH E:943	BINDING SITE FOR RESIDUE SO4 E 801
13	BC4	SOFTWARE	GLY D:138 , PHE D:139 , ARG D:142 , GLY E:138 , PHE E:139 , ARG E:142 , GLU E:149 , GLY F:138 , PHE F:139 , ARG F:142 , GLU F:149 , HOH F:948	BINDING SITE FOR RESIDUE GPP F 902

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

Asymmetric Unit

No.	Residues
1	Gly A:16	-	Pro A:17
2	Ala A:102	-	Pro A:103
3	Gly B:16	-	Pro B:17
4	Ala B:102	-	Pro B:103
5	Gly C:16	-	Pro C:17
6	Ala C:102	-	Pro C:103
7	Gly D:16	-	Pro D:17
8	Ala D:102	-	Pro D:103
9	Gly E:16	-	Pro E:17
10	Ala E:102	-	Pro E:103
11	Ala F:102	-	Pro F:103

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

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPF	PS01350	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.	ISPF_ECOLI	35-50	6	A:35-50 B:35-50 C:35-50 D:35-50 E:35-50 F:35-50

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPF	PS01350	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.	ISPF_ECOLI	35-50	3	A:35-50 B:35-50 C:35-50 - - -

Biological Unit 2 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPF	PS01350	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.	ISPF_ECOLI	35-50	3	- - - D:35-50 E:35-50 F:35-50

(no "Exon" information available for 3ERN)

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:157
 aligned with ISPF_ECOLI | P62617 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
           ISPF_ECOLI     - -MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
               SCOP domains d3erna_ A: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                          SCOP domains
               CATH domains 3ernA00 A:0-156  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee....eee..eee....eee.....hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhh...eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ern A   0 EMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with ISPF_ECOLI | P62617 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
           ISPF_ECOLI     - -MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
               SCOP domains d3ernb_ B: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                          SCOP domains
               CATH domains 3ernB00 B:0-156  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee..eee..eee...eee......hhhhhhhhhhhhhh....hhhhhh..........hhhhhhhhhhhhhhh...eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ern B   0 EMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with ISPF_ECOLI | P62617 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
           ISPF_ECOLI     - -MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
               SCOP domains d3ernc_ C: 2C-methyl-D-erythr      itol 2,4-cyclodiphosphate synthase IspF                                                                                    SCOP domains
               CATH domains 3ernC00 C:0-156  [code=3.30.1      330.50, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee......eee..eee...------...hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ern C   0 EMRIGHGFDVHAFGGEGPIIIGGVRIPYE------SDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
                                     9        19        |-     |  39        49        59        69        79        89        99       109       119       129       139       149       
                                                       28     35

Chain D from PDB  Type:PROTEIN  Length:157
 aligned with ISPF_ECOLI | P62617 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
           ISPF_ECOLI     - -MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
               SCOP domains d3ernd_ D: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                          SCOP domains
               CATH domains 3ernD00 D:0-156  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee....eee..eee....ee......hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhh...eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ern D   0 EMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149

Chain E from PDB  Type:PROTEIN  Length:157
 aligned with ISPF_ECOLI | P62617 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
           ISPF_ECOLI     - -MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
               SCOP domains d3erne_ E: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                          SCOP domains
               CATH domains 3ernE00 E:0-156  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee......eee..eee............hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ern E   0 EMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149

Chain F from PDB  Type:PROTEIN  Length:148
 aligned with ISPF_ECOLI | P62617 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
           ISPF_ECOLI     - -MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
               SCOP domains d3ernf_ F: 2C-   methyl-D-er      ythritol 2,4-cyclodiphosphate synthase IspF                                                                                 SCOP domains
               CATH domains 3ernF00 F:0-15   6  [code=3.      30.1330.50, no name defined]                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..---.eee..eee..------....hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhh...eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ern F   0 EMRIGHGFDVHAFG---PIIIGGVRIPY------HSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
                                     9   |   |19       | -    |   39        49        59        69        79        89        99       109       119       129       139       149       
                                        13  17        27     34

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) (23004)

Fold: Bacillus chorismate mutase-like (324)

Superfamily: IpsF-like (56)

Family: IpsF-like (35)

Protein domain: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (27)

Escherichia coli K-12 [TaxId: 83333] (5)

1a	d3erna_	A:
1b	d3ernb_	B:
1c	d3ernc_	C:
1d	d3ernd_	D:
1e	d3erne_	E:
1f	d3ernf_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: [code=3.30.1330.50, no name defined] (46)

Escherichia coli k-12. Organism_taxid: 83333. Strain: k12. (4)

1a	3ernC00	C:0-156
1b	3ernA00	A:0-156
1c	3ernB00	B:0-156
1d	3ernD00	D:0-156
1e	3ernE00	E:0-156
1f	3ernF00	F:0-156

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (ISPF_ECOLI | P62617)

molecular function
	GO:0008685	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity	Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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: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.
	GO:0006744	ubiquinone biosynthetic process	The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:102 - Pro A:103	[ RasMol ]
		Ala B:102 - Pro B:103	[ RasMol ]
		Ala C:102 - Pro C:103	[ RasMol ]
		Ala D:102 - Pro D:103	[ RasMol ]
		Ala E:102 - Pro E:103	[ RasMol ]
		Ala F:102 - Pro F:103	[ RasMol ]
		Gly A:16 - Pro A:17	[ RasMol ]
		Gly B:16 - Pro B:17	[ RasMol ]
		Gly C:16 - Pro C:17	[ RasMol ]
		Gly D:16 - Pro D:17	[ RasMol ]
		Gly E:16 - Pro E:17	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
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	4.6.1.12
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(no "Related Entries Specified in the PDB File" available for 3ERN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (11, 11)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 6)

CATH Domains (1, 6)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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Still Images

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Databases

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File