4C8G - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ISPF (BURKHOLDERIA CENOCEPACIA) CMP COMPLEX

Authors :   P. E. F. O'Rourke, J. Kalinowska-Tluscik, P. K. Fyfe, A. Dawson, W. N. Hu

Date :   01 Oct 13 (Deposition) - 08 Jan 14 (Release) - 29 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. E. F. O'Rourke, J. Kalinowska-Tluscik, P. K. Fyfe, A. Dawson, W. N. Hunter
Crystal Structures Of Ispf From Plasmodium Falciparum And Burkholderia Cenocepacia: Comparisons Inform Antimicrobial Drug Target Assessment.
Bmc Struct. Biol. V. 14 1 2014
PubMed-ID: 24410837 | Reference-DOI: 10.1186/1472-6807-14-1

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
	Chains	:	A, B, C
	EC Number	:	4.6.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	GOLD
	Expression System Vector	:	PET15BTEV
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BURKHOLDERIA CENOCEPACIA
	Organism Taxid	:	216591
	Other Details	:	GENOMIC DNA
	Strain	:	J2315
	Synonym	:	MECDP-SYNTHASE, MECPP-SYNTHASE, MECPS, 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	C5P	3	Ligand/Ion	CYTIDINE-5'-MONOPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	PO4	1	Ligand/Ion	PHOSPHATE ION
4	ZN	3	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:10 , HIS A:12 , HIS A:44	BINDING SITE FOR RESIDUE ZN A1162
2	AC2	SOFTWARE	ASP B:10 , HIS B:12 , HIS B:44 , HOH B:2012	BINDING SITE FOR RESIDUE ZN B1162
3	AC3	SOFTWARE	ASP C:10 , HIS C:12 , HIS C:44	BINDING SITE FOR RESIDUE ZN C1162
4	AC4	SOFTWARE	ASP B:58 , ILE B:59 , GLY B:60 , HOH B:2011 , HOH B:2012 , HOH B:2028 , ALA C:102 , PRO C:105 , LYS C:106 , LEU C:107 , ALA C:108 , ALA C:133 , LYS C:134 , THR C:135 , HOH C:2037	BINDING SITE FOR RESIDUE C5P C1163
5	AC5	SOFTWARE	ALA A:102 , PRO A:105 , LYS A:106 , LEU A:107 , ALA A:108 , ALA A:133 , LYS A:134 , THR A:135 , HOH A:2058 , HOH A:2059 , HOH A:2072 , HOH A:2073 , ASP C:58 , GLY C:60	BINDING SITE FOR RESIDUE C5P A1163
6	AC6	SOFTWARE	ASP A:58 , GLY A:60 , HOH A:2009 , HOH A:2011 , HOH A:2026 , HOH A:2029 , ALA B:102 , PRO B:105 , LYS B:106 , LEU B:107 , ALA B:108 , ALA B:133 , LYS B:134 , THR B:135 , HOH B:2051 , HOH B:2060	BINDING SITE FOR RESIDUE C5P B1163
7	AC7	SOFTWARE	GLY A:140 , TYR A:141 , GLY B:140 , TYR B:141 , HOH B:2055 , HOH B:2063 , GLY C:140 , TYR C:141	BINDING SITE FOR RESIDUE PO4 B1164
8	AC8	SOFTWARE	HOH A:2067 , HOH A:2068 , HOH B:2056 , HOH B:2057 , HOH C:2035 , HOH C:2036	BINDING SITE FOR RESIDUE MG B1165

(no "SS Bond" information available for 4C8G)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:104	-	Pro A:105
2	Gln A:159	-	Gly A:160
3	Ala B:104	-	Pro B:105
4	Gln B:159	-	Gly B:160
5	Ala C:104	-	Pro C:105
6	Gln C:159	-	Gly C:160

(no "SAP(SNP)/Variant" information available for 4C8G)

Asymmetric/Biological 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_BURCJ	37-52	3	A:37-52 B:38-52 C:37-52

(no "Exon" information available for 4C8G)

Asymmetric/Biological 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:153
 aligned with ISPF_BURCJ | B4EC22 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
           ISPF_BURCJ     1 MDFRIGQGYDVHQLVEGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDAAFKGADSRVLLRACAERVKAAGFTIQNVDSTVIAQAPKLAPHIDGMRANIAADLGLPLERVNVKAKTNEKLGYLGRGEGIEAQAAALLVKQGG 161
               SCOP domains d4c8ga_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee...eee..eee...eee......hhhhhhhhhhhhhhh...hhhhh.--------..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c8g A   1 MDVRIGQGYDVHQLVEGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHF--------GADSRVLLRACAERVKAAGFTIQNVDSTVIAQAPKLAPHIDGMRANIAADLGLPLERVNVKAKTNEKLGYLGRGEGIEAQAAALLVKQGG 161
                                    10        20        30        40        50        60  |      - |      80        90       100       110       120       130       140       150       160 
                                                                                         63       72

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with ISPF_BURCJ | B4EC22 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
           ISPF_BURCJ     1 MDFRIGQGYDVHQLVEGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDAAFKGADSRVLLRACAERVKAAGFTIQNVDSTVIAQAPKLAPHIDGMRANIAADLGLPLERVNVKAKTNEKLGYLGRGEGIEAQAAALLVKQGG 161
               SCOP domains d4c8gb_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eee..eee....ee..--..hhhhhhhhhhhhhhh...hhhhhh.-------..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c8g B   1 MDVRIGQGYDVHQLVEGRPLIIGGVTIPYERGLLG--DADVLLHAITDALFGAAALGDIGRHFS-------GADSRVLLRACAERVKAAGFTIQNVDSTVIAQAPKLAPHIDGMRANIAADLGLPLERVNVKAKTNEKLGYLGRGEGIEAQAAALLVKQGG 161
                                    10        20        30    |  |40        50        60   |     - |      80        90       100       110       120       130       140       150       160 
                                                             35 38                        64      72

Chain C from PDB  Type:PROTEIN  Length:153
 aligned with ISPF_BURCJ | B4EC22 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
           ISPF_BURCJ     1 MDFRIGQGYDVHQLVEGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDAAFKGADSRVLLRACAERVKAAGFTIQNVDSTVIAQAPKLAPHIDGMRANIAADLGLPLERVNVKAKTNEKLGYLGRGEGIEAQAAALLVKQGG 161
               SCOP domains d4c8gc_ C: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee....ee..ee....eeee.....hhhhhhhhhhhhhhh...hhhhhh..--------hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhh...eee....hhhhhh..eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c8g C   1 MDVRIGQGYDVHQLVEGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSD--------DSRVLLRACAERVKAAGFTIQNVDSTVIAQAPKLAPHIDGMRANIAADLGLPLERVNVKAKTNEKLGYLGRGEGIEAQAAALLVKQGG 161
                                    10        20        30        40        50        60    |    -   |    80        90       100       110       120       130       140       150       160 
                                                                                           65       74

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/Biological 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: automated matches (21)

Protein domain: automated matches (21)

Burkholderia cenocepacia [TaxId: 216591] (3)

1a	d4c8ga_	A:
1b	d4c8gb_	B:
1c	d4c8gc_	C:

(no "CATH Domain" information available for 4C8G)

(no "Pfam Domain" information available for 4C8G)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (ISPF_BURCJ | B4EC22)

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/Biological Unit
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	Cis Peptide Bonds
		Ala A:104 - Pro A:105	[ RasMol ]
		Ala B:104 - Pro B:105	[ RasMol ]
		Ala C:104 - Pro C:105	[ RasMol ]
		Gln A:159 - Gly A:160	[ RasMol ]
		Gln B:159 - Gly B:160	[ RasMol ]
		Gln C:159 - Gly C:160	[ RasMol ]

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	ISPF_BURCJ \| B4EC22	:	4c8e 4c8i

4c81	ISPF (PLASMODIUM FALCIPARUM) CDP COMPLEX
4c82	ISPF (PLASMODIUM FALCIPARUM) UNLIGANDED STRUCTURE
4c8e	ISPF (BURKHOLDERIA CENOCEPACIA) 2CMP COMPLEX
4c8i	ISPF (BURKHOLDERIA CENOCEPACIA) CITRATE COMPLEX RELATED ENTRIES

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

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SCOP Domains (1, 3)

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Gene Ontology (6, 6)

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