2V2V - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   ISPE IN COMPLEX WITH LIGAND

Authors :   M. S. Alphey, W. N. Hunter

Date :   07 Jun 07 (Deposition) - 19 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Transferase, 4-Diphosphocytidyl-2C-Methyl-D- Erythritol, Aquifex Aeolicus, Nucleotide-Binding, Isoprene Biosynthesis, Kinase, Atp-Binding, Non-Mevalonate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. M. Crane, A. K. Hirsch, M. S. Alphey, T. Sgraja, S. Lauw, V. Illarionova, F. Rohdich, W. Eisenreich, W. N. Hunter, A. Bacher, F. Diederich
Synthesis And Characterization Of Cytidine Derivatives That Inhibit The Kinase Ispe Of The Non-Mevalonate Pathway For Isoprenoid Biosynthesis.
Chemmedchem V. 3 91 2008
PubMed-ID: 18033714 | Reference-DOI: 10.1002/CMDC.200700208

Molecule 1 - 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.148
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	CMK, 4-CYTIDINE-5'-DIPHOSPHO-2-C-METHYL-D -ERYTHRITOL KINASE

		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 (4, 18)

No.	Name	Count	Type	Full Name
1	BR	8	Ligand/Ion	BROMIDE ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	SO4	5	Ligand/Ion	SULFATE ION
4	V12	2	Ligand/Ion	5'-[(1H-BENZIMIDAZOL-2-YLACETYL)AMINO]-5'-DEOXYCYTIDINE

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	2	Ligand/Ion	SULFATE ION
4	V12	1	Ligand/Ion	5'-[(1H-BENZIMIDAZOL-2-YLACETYL)AMINO]-5'-DEOXYCYTIDINE

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	SO4	3	Ligand/Ion	SULFATE ION
4	V12	1	Ligand/Ion	5'-[(1H-BENZIMIDAZOL-2-YLACETYL)AMINO]-5'-DEOXYCYTIDINE

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:90 , ALA A:91 , GLY A:92 , LEU A:93 , GLY A:94 , V12 A:1277 , HOH A:2049 , HOH A:2124 , HOH A:2125	BINDING SITE FOR RESIDUE SO4 A1269
02	AC2	SOFTWARE	ARG A:213 , TYR A:223 , ARG A:224	BINDING SITE FOR RESIDUE SO4 A1270
03	AC3	SOFTWARE	GLU A:218	BINDING SITE FOR RESIDUE BR A1272
04	AC4	SOFTWARE	ASN A:206 , PHE A:234 , VAL A:235 , HOH A:2091	BINDING SITE FOR RESIDUE BR A1273
05	AC5	SOFTWARE	ARG A:19 , GLU A:180 , GLY B:18 , ARG B:19	BINDING SITE FOR RESIDUE BR A1274
06	AC6	SOFTWARE	MET A:1 , TYR A:41 , GLU A:221 , ARG A:259	BINDING SITE FOR RESIDUE BR A1275
07	AC7	SOFTWARE	ARG A:43 , ASN A:220	BINDING SITE FOR RESIDUE BR A1276
08	AC8	SOFTWARE	PRO B:89 , GLY B:90 , GLY B:95 , GLY B:96 , GOL B:1273 , HOH B:2131 , HOH B:2132 , HOH B:2133 , HOH B:2134	BINDING SITE FOR RESIDUE SO4 B1269
09	AC9	SOFTWARE	LYS B:9 , GLY B:92 , ASP B:130 , THR B:171 , GLY B:237 , SER B:238 , GLY B:239 , GOL B:1272 , HOH B:2134	BINDING SITE FOR RESIDUE SO4 B1270
10	BC1	SOFTWARE	ARG B:213 , TYR B:223 , ARG B:224	BINDING SITE FOR RESIDUE SO4 B1271
11	BC2	SOFTWARE	PRO B:217 , GLU B:218	BINDING SITE FOR RESIDUE BR B1274
12	BC3	SOFTWARE	PHE B:234 , VAL B:235 , HOH B:2103	BINDING SITE FOR RESIDUE BR B1275
13	BC4	SOFTWARE	ARG B:43 , PRO B:89	BINDING SITE FOR RESIDUE BR B1276
14	BC5	SOFTWARE	TYR A:24 , HIS A:25 , LYS A:145 , SER A:168 , SER A:169 , SER A:170 , THR A:171 , TYR A:175 , SO4 A:1269	BINDING SITE FOR RESIDUE V12 A1277
15	BC6	SOFTWARE	TYR B:24 , HIS B:25 , LYS B:145 , SER B:170 , THR B:171 , GLY B:172 , ARG B:173 , TYR B:175 , SER B:176 , GOL B:1272 , HOH B:2135 , HOH B:2136	BINDING SITE FOR RESIDUE V12 B1277
16	BC7	SOFTWARE	ILE A:55 , ASN A:60 , LEU A:61 , LYS A:85 , GLY A:96 , ASN A:99	BINDING SITE FOR RESIDUE GOL A1271
17	BC8	SOFTWARE	LYS B:9 , ASN B:11 , LEU B:14 , ASP B:130 , TYR B:175 , GLY B:237 , SO4 B:1270 , V12 B:1277	BINDING SITE FOR RESIDUE GOL B1272
18	BC9	SOFTWARE	ILE B:55 , ASN B:60 , LEU B:61 , LYS B:85 , GLY B:96 , ASN B:99 , SO4 B:1269	BINDING SITE FOR RESIDUE GOL B1273

(no "SS Bond" information available for 2V2V)

Asymmetric Unit

No.	Residues
1	Ser A:-1	-	His A:0
2	Gly A:239	-	Ser A:240
3	Gly B:239	-	Ser B:240

(no "SAP(SNP)/Variant" information available for 2V2V)

(no "PROSITE Motif" information available for 2V2V)

(no "Exon" information available for 2V2V)

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:270
 aligned with ISPE_AQUAE | O67060 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:270
                              1                                                                                                                                                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268
           ISPE_AQUAE     - --MIKVLSPAKINLGLWVLGRLPSGYHEILTLYQEIPFYDEIYIREGVLRVETNIGIPQEENLVYKGLREFERITGIEINYSIFIQKNIPPGAGLGGGSSNLAVVLKKVNELLGSPLSEEELRELVGSISADAPFFLLGKSAIGRGKGEVLEPVETEISGKITLVIPQVSSSTGRVYSSLREEHFVTPEYAEEKIQRIISGEVEEIENVLGDIARELYPEINEVYRFVEYLGFKPFVSGSGSTVYFFGGASEELKKAAKMRGWKVVELEL 268
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeee...eeee........hhhhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhh.eeeee....eeee......eeeeeee.....hhhhhhh..hhhh..hhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....ee......eee....hhhhhhhhhhhh.eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2v2v A  -1 SHMIKVLSPAKINLGLWVLGRLPSGYHEILTLYQEIPFYDEIYIREGVLRVETNIGIPQEENLVYKGLREFERITGIEINYSIFIQKNIPPGAGLGGGSSNLAVVLKKVNELLGSPLSEEELRELVGSISADAPFFLLGKSAIGRGKGEVLEPVETEISGKITLVIPQVSSSTGRVYSSLREEHFVTPEYAEEKIQRIISGEVEEIENVLGDIARELYPEINEVYRFVEYLGFKPFVSGSGSTVYFFGGASEELKKAAKMRGWKVVELEL 268
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268

Chain B from PDB  Type:PROTEIN  Length:270
 aligned with ISPE_AQUAE | O67060 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:270
                              1                                                                                                                                                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268
           ISPE_AQUAE     - --MIKVLSPAKINLGLWVLGRLPSGYHEILTLYQEIPFYDEIYIREGVLRVETNIGIPQEENLVYKGLREFERITGIEINYSIFIQKNIPPGAGLGGGSSNLAVVLKKVNELLGSPLSEEELRELVGSISADAPFFLLGKSAIGRGKGEVLEPVETEISGKITLVIPQVSSSTGRVYSSLREEHFVTPEYAEEKIQRIISGEVEEIENVLGDIARELYPEINEVYRFVEYLGFKPFVSGSGSTVYFFGGASEELKKAAKMRGWKVVELEL 268
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------GHMP_kinases_N-2v2vB01 B:80-138                            ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------GHMP_kinases_N-2v2vB02 B:80-138                            ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeee...eeee....hhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhh..eeeee....eeeee.....eeeeeee.....hhhhhhh..hhhhh.hhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....ee......eee....hhhhhhhhhhhh.eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2v2v B  -1 SHMIKVLSPAKINLGLWVLGRLPSGYHEILTLYQEIPFYDEIYIREGVLRVETNIGIPQEENLVYKGLREFERITGIEINYSIFIQKNIPPGAGLGGGSSNLAVVLKKVNELLGSPLSEEELRELVGSISADAPFFLLGKSAIGRGKGEVLEPVETEISGKITLVIPQVSSSTGRVYSSLREEHFVTPEYAEEKIQRIISGEVEEIENVLGDIARELYPEINEVYRFVEYLGFKPFVSGSGSTVYFFGGASEELKKAAKMRGWKVVELEL 268
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268

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 2V2V)

(no "CATH Domain" information available for 2V2V)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: S5 (103)

Family: GHMP_kinases_N (23)

Aquifex aeolicus (5)

1a	GHMP_kinases_N-2v2vB01	B:80-138
1b	GHMP_kinases_N-2v2vB02	B:80-138

Asymmetric Unit(hide GO term definitions)

Chain A,B (ISPE_AQUAE | O67060)

molecular function
	GO:0050515	4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity	Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + 2 H(+).
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	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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	Cis Peptide Bonds
		Gly A:239 - Ser A:240	[ RasMol ]
		Gly B:239 - Ser B:240	[ RasMol ]
		Ser A:-1 - His A:0	[ RasMol ]

Biological Units
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	2v2v
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	2.7.1.148
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	ISPE_AQUAE \| O67060
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UniProtKB/Swiss-Prot
	ISPE_AQUAE \| O67060	:	2v2q 2v2z 2v34 2v8p 2vf3

2v2q	ISPE IN COMPLEX WITH LIGAND
2v2z	ISPE IN COMPLEX WITH ADP AND CDPME
2v34	ISPE IN COMPLEX WITH CYTIDINE AND LIGAND
2v8p	ISPE IN COMPLEX WITH ADP AND CDP
2vf3	AQUIFEX AEOLICUS ISPE IN COMPLEX WITH LIGAND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Pfam Domains (1, 2)

Gene Ontology (9, 9)

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