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Title :   STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE FROM HAEMOPHILUS INFLUENZAE (HI0671)

Authors :   C. Lehmann, K. Lim, J. Toedt, W. Krajewski, A. Howard, E. Eisenstein, O. Herzberg, Structure 2 Function Project (S2F)

Date :   21 Jul 01 (Deposition) - 21 Aug 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   2C-Methyl-D-Erythritol 2, 4-Cyclodiphosphate Synthase, Mecps, Isoprenoid Biosynthesis, Structural Genomics, Structure 2 Function Project, S2F, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Lehmann, K. Lim, J. Toedt, W. Krajewski, A. Howard, E. Eisenstein, O. Herzberg
Structure Of 2C-Methyl-D-Erythrol-2, 4-Cyclodiphosphate Synthase From Haemophilus Influenzae: Activation By Conformational Transition.
Proteins V. 49 135 2002
PubMed-ID: 12211023 | Reference-DOI: 10.1002/PROT.10182
(for further references see the PDB file header)

Molecule 1 - 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
	Chains	:	A, B, C
	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	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727
	Synonym	:	MECPS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CO	4	Ligand/Ion	COBALT (II) ION
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:9 , HIS A:11 , HIS A:35 , HIS A:43	BINDING SITE FOR RESIDUE CO A 201
2	AC2	SOFTWARE	ASP B:9 , HIS B:11 , HIS B:35 , HIS B:43	BINDING SITE FOR RESIDUE CO B 202
3	AC3	SOFTWARE	ASP C:9 , HIS C:11 , HIS C:35 , HIS C:43	BINDING SITE FOR RESIDUE CO C 203
4	AC4	SOFTWARE	GLU A:150 , GLU B:150 , HIS C:6 , GLU C:150	BINDING SITE FOR RESIDUE CO C 204
5	AC5	SOFTWARE	GLY A:139 , PHE A:140 , ARG A:143 , ARG B:143 , GLY C:139 , ARG C:143	BINDING SITE FOR RESIDUE SO4 A 301

(no "SS Bond" information available for 1JN1)

(no "Cis Peptide Bond" information available for 1JN1)

(no "SAP(SNP)/Variant" information available for 1JN1)

Asymmetric Unit (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_HAEIN	36-51	3	A:36-51 B:36-51 C:36-51

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_HAEIN	36-51	3	A:36-51 B:36-51 C:36-51

Biological Unit 2 (1, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPF	PS01350	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.	ISPF_HAEIN	36-51	12	A:36-51 B:36-51 C:36-51

(no "Exon" information available for 1JN1)

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_HAEIN | P44815 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           ISPF_HAEIN     1 MIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFPDTDMQYKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIR 157
               SCOP domains d1jn1a_ A: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                          SCOP domains
               CATH domains 1jn1A00 A:1-157  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..................hhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeeeeeeeee........hhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jn1 A   1 MIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFPDTDMQYKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIR 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with ISPF_HAEIN | P44815 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           ISPF_HAEIN     1 MIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFPDTDMQYKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIR 157
               SCOP domains d1jn1b_ B: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                          SCOP domains
               CATH domains 1jn1B00 B:1-157  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee.......ee..ee.............hhhhhhhhhhhhhhhh..hhhhhh..hhhhh...hhhhhhhhhhhhhhh...eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jn1 B   1 MIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFPDTDMQYKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIR 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:157
 aligned with ISPF_HAEIN | P44815 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           ISPF_HAEIN     1 MIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFPDTDMQYKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIR 157
               SCOP domains d1jn1c_ C: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                          SCOP domains
               CATH domains 1jn1C00 C:1-157  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
           Pfam domains (1) -YgbB-1jn1C01 C:2-157                                                                                                                                         Pfam domains (1)
           Pfam domains (2) -YgbB-1jn1C02 C:2-157                                                                                                                                         Pfam domains (2)
           Pfam domains (3) -YgbB-1jn1C03 C:2-157                                                                                                                                         Pfam domains (3)
         Sec.struct. author .eeeeeeeeeee..................hhhhhh..hhhhhhhhhhhhhhhh..hhhhhh..hhhhh...hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jn1 C   1 MIRIGHGFDVHAFGEDRPLIIGGVEVPYHTGFIAHSDGDVALHALTDAILGAAALGDIGKLFPDTDMQYKNADSRGLLREAFRQVQEKGYKIGNVDITIIAQAPKMRPHIDAMRAKIAEDLQCDIEQVNVKATTTEKLGFTGRQEGIACEAVALLIR 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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(

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Folds(

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Superfamilies( (-)

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Families(

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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)

Haemophilus influenzae [TaxId: 727] (3)

1a	d1jn1a_	A:
1b	d1jn1b_	B:
1c	d1jn1c_	C:

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)

Haemophilus influenzae. Organism_taxid: 727. (3)

1a	1jn1A00	A:1-157
1b	1jn1B00	B:1-157
1c	1jn1C00	C:1-157

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: YgbB] (24)

Family: YgbB (24)

Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (3)

1a	YgbB-1jn1C01	C:2-157
1b	YgbB-1jn1C02	C:2-157
1c	YgbB-1jn1C03	C:2-157

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (ISPF_HAEIN | P44815)

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: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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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.

Asymmetric Unit
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Description

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