1OJ4 - JenaLib

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Title :   TERNARY COMPLEX OF 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE

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

Date :   30 Jun 03 (Deposition) - 31 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

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

Keywords :   Transferase, Kinase, Isoprenoids Biosynthesis, Ghmp Kinase Superfamily Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Miallau, M. S. Alphey, L. E. Kemp, G. A. Leonard, S. M. Mcsweeney, S. Hecht, A. Bacher, W. Eisenreich, F. Rohdich, W. N. Hunter
Biosynthesis Of Isoprenoids: Crystal Structure Of 4-Diphosphocytidyl-2C-Methyl-D-Erythritol Kinase
Proc. Natl. Acad. Sci. Usa V. 100 9173 2003
PubMed-ID: 12878729 | Reference-DOI: 10.1073/PNAS.1533425100

Molecule 1 - 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.148
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PET15B
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	217992
	Strain	:	O6
	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, 17)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	CDM	2	Ligand/Ion	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
3	CL	1	Ligand/Ion	CHLORIDE ION
4	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	CDM	1	Ligand/Ion	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	CDM	1	Ligand/Ion	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:147 , HOH A:2095 , HOH A:2096	BINDING SITE FOR RESIDUE CL A1286
2	AC2	SOFTWARE	LYS A:10 , ASN A:12 , GLY A:24 , TYR A:25 , HIS A:26 , GLY A:139 , ALA A:140 , ASP A:141 , VAL A:156 , THR A:181 , PHE A:185 , ANP A:1285 , HOH A:2093 , HOH A:2101 , HOH A:2184 , HOH A:2185 , HOH A:2186 , HOH A:2187 , HOH A:2188 , HOH A:2189 , HOH A:2190	BINDING SITE FOR RESIDUE CDM A1284
3	AC3	SOFTWARE	LYS A:10 , VAL A:60 , ASN A:65 , LEU A:66 , LYS A:96 , MSE A:100 , GLY A:101 , GLY A:102 , GLY A:103 , LEU A:104 , GLY A:105 , GLY A:106 , GLY A:107 , SER A:108 , ASN A:110 , CDM A:1284 , HOH A:2068 , HOH A:2184 , HOH A:2188 , HOH A:2190 , HOH A:2192	BINDING SITE FOR RESIDUE ANP A1285
4	AC4	SOFTWARE	LYS B:10 , ASN B:12 , GLY B:24 , TYR B:25 , HIS B:26 , LEU B:28 , PHE B:32 , SER B:108 , ALA B:140 , ASP B:141 , VAL B:156 , THR B:181 , PHE B:185 , THR B:240 , ANP B:1285 , HOH B:2104 , HOH B:2186 , HOH B:2187 , HOH B:2188 , HOH B:2189 , HOH B:2190	BINDING SITE FOR RESIDUE CDM B1284
5	AC5	SOFTWARE	ASP B:64 , ASN B:65 , LEU B:66 , LYS B:96 , PRO B:99 , MSE B:100 , GLY B:101 , GLY B:103 , LEU B:104 , GLY B:105 , GLY B:106 , GLY B:107 , SER B:108 , ASN B:110 , CDM B:1284 , HOH B:2189 , HOH B:2190 , HOH B:2191	BINDING SITE FOR RESIDUE ANP B1285

(no "SS Bond" information available for 1OJ4)

Asymmetric Unit

No.	Residues
1	Gly A:241	-	Ala A:242
2	Gly B:241	-	Ala B:242

(no "SAP(SNP)/Variant" information available for 1OJ4)

(no "PROSITE Motif" information available for 1OJ4)

(no "Exon" information available for 1OJ4)

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:283
 aligned with ISPE_ECOL6 | Q8FI04 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:283
                                    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   
           ISPE_ECOL6     1 MRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLMKTAADSGRLSTGSGANISIDKRLPMGGGLGGGSSNAATVLVALNHLWQCGLSMDELAEMGLTLGADVPVFVRGHAAFAEGVGEILMPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGVNLSPLHRAML 283
               SCOP domains d1oj4a1 A:1-163 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                                                                       d1oj4a2 A:164-283 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                           SCOP domains
               CATH domains -1oj4A01 A:2-164  [code=3.30.230.10, no name defined]                                                                                                               ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeee..............hhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhh..eeee....eeee......eeeee......hhhhhhh...........hhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....eee......eeeee.hhhhhhhhhhhhhhhhh.eeeeee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oj4 A   1 mRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLmKTAADSGRLPTGSGANISIDKRLPmGGGLGGGSSNAATVLVALNHLWQCGLSmDELAEmGLTLGADVPVFVRGHAAFAEGVGEILTPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGVNLSPLHRAmL 283
                            |       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 | 
                            |                                                                        75-MSE                  100-MSE                     128-MSE |                                                                                                                                                 282-MSE
                            1-MSE                                                                                                                              134-MSE

Chain B from PDB  Type:PROTEIN  Length:283
 aligned with ISPE_ECOL6 | Q8FI04 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:283
                                    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   
           ISPE_ECOL6     1 MRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLMKTAADSGRLSTGSGANISIDKRLPMGGGLGGGSSNAATVLVALNHLWQCGLSMDELAEMGLTLGADVPVFVRGHAAFAEGVGEILMPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGVNLSPLHRAML 283
               SCOP domains d1oj4b1 B:1-163 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                                                                       d1oj4b2 B:164-283 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                           SCOP domains
               CATH domains -1oj4B01 B:2-164  [code=3.30.230.10, no name defined]                                                                                                               ----------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------GHMP_kinases_N-1oj4B01 B:91-149                            -----------------------------------------GHMP_kinases_C-1oj4B03 B:191-266                                            ----------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------GHMP_kinases_N-1oj4B02 B:91-149                            -----------------------------------------GHMP_kinases_C-1oj4B04 B:191-266                                            ----------------- Pfam domains (2)
         Sec.struct. author ..eeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeee..............hhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhh..eeee....eeee......eeeee......hhhhhhh...........hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eee......eeeee.hhhhhhhhhhhhhhhhh.eeeeee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oj4 B   1 mRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLmKTAADSGRLPTGSGANISIDKRLPmGGGLGGGSSNAATVLVALNHLWQCGLSmDELAEmGLTLGADVPVFVRGHAAFAEGVGEILTPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGVNLSPLHRAmL 283
                            |       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 | 
                            |                                                                        75-MSE                  100-MSE                     128-MSE |                                                                                                                                                 282-MSE
                            1-MSE                                                                                                                              134-MSE

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Ribosomal Protein S5; domain 2 (189)

Homologous Superfamily: [code=3.30.230.10, no name defined] (170)

Escherichia coli. Organism_taxid: 217992. Strain: o6. (1)

1a	1oj4A01	A:2-164
1b	1oj4B01	B:2-164

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: S5 (103)

Family: GHMP_kinases_N (23)

Escherichia coli O6 (1)

1a	GHMP_kinases_N-1oj4B01	B:91-149
1b	GHMP_kinases_N-1oj4B02	B:91-149

Clan: no clan defined [family: GHMP_kinases_C] (13)

Family: GHMP_kinases_C (13)

Escherichia coli O6 (1)

2a	GHMP_kinases_C-1oj4B03	B:191-266
2b	GHMP_kinases_C-1oj4B04	B:191-266

Asymmetric Unit(hide GO term definitions)

Chain A,B (ISPE_ECOL6 | Q8FI04)

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.

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	Cis Peptide Bonds
		Gly A:241 - Ala A:242	[ RasMol ]
		Gly B:241 - Ala B:242	[ RasMol ]

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	1oj4
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Description

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Ligands, Modified Residues, Ions (4, 17)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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