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Title :   X-RAY STRUCTURE OF ACANTHAMOEBA PLOYPHAGA MIMIVIRUS NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH UDP

Authors :   S. Jeudy, A. Lartigue, J. M. Claverie, C. Abergel

Date :   15 Sep 08 (Deposition) - 16 Jun 09 (Release) - 25 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Ndk Phosphotransferase Nucleotide Binding, Atp-Binding, Kinase, Magnesium, Metal-Binding, Nucleotide Metabolism, Nucleotide-Binding, Phosphoprotein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Jeudy, A. Lartigue, J. M. Claverie, C. Abergel
Dissecting The Unique Nucleotide Specificity Of Mimivirus Nucleoside Diphosphate Kinase.
J. Virol. V. 83 7142 2009
PubMed-ID: 19439473 | Reference-DOI: 10.1128/JVI.00511-09
(for further references see the PDB file header)

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	2.7.4.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDIGS02
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NDK, MIMI_R418
	Organism Scientific	:	ACANTHAMOEBA POLYPHAGA MIMIVIRUS
	Organism Taxid	:	212035
	Synonym	:	NDP KINASE, NDK

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	MG	6	Ligand/Ion	MAGNESIUM ION
2	UDP	6	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	UDP	6	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	UDP	6	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:86 , UDP A:161	BINDING SITE FOR RESIDUE MG A 160
02	AC2	SOFTWARE	ARG B:86 , UDP B:162	BINDING SITE FOR RESIDUE MG B 161
03	AC3	SOFTWARE	ARG C:86 , UDP C:163	BINDING SITE FOR RESIDUE MG C 162
04	AC4	SOFTWARE	UDP D:164	BINDING SITE FOR RESIDUE MG D 163
05	AC5	SOFTWARE	UDP E:165	BINDING SITE FOR RESIDUE MG E 164
06	AC6	SOFTWARE	ARG F:86 , UDP F:166	BINDING SITE FOR RESIDUE MG F 165
07	AC7	SOFTWARE	LYS A:9 , HIS A:53 , TYR A:58 , ASN A:62 , ARG A:86 , GLN A:89 , ARG A:99 , ILE A:106 , ARG A:107 , ASN A:109 , MG A:160 , HOH A:195 , HOH A:196	BINDING SITE FOR RESIDUE UDP A 161
08	AC8	SOFTWARE	LYS B:9 , TYR B:50 , HIS B:53 , TYR B:58 , ASN B:62 , ARG B:86 , ARG B:99 , ILE B:106 , ARG B:107 , ASN B:109 , MG B:161 , HOH B:171	BINDING SITE FOR RESIDUE UDP B 162
09	AC9	SOFTWARE	LYS C:9 , TYR C:50 , HIS C:53 , TYR C:58 , ASN C:62 , ARG C:86 , ARG C:99 , ILE C:106 , ARG C:107 , ASN C:109 , MG C:162 , HOH C:188 , HOH C:207	BINDING SITE FOR RESIDUE UDP C 163
10	BC1	SOFTWARE	LYS D:9 , TYR D:50 , HIS D:53 , TYR D:58 , ASN D:62 , ARG D:86 , GLN D:89 , ARG D:99 , ILE D:106 , ARG D:107 , ASN D:109 , MG D:163 , HOH D:168 , HOH D:198	BINDING SITE FOR RESIDUE UDP D 164
11	BC2	SOFTWARE	LYS E:9 , HIS E:53 , TYR E:58 , ASN E:62 , ARG E:86 , ARG E:99 , ILE E:106 , ARG E:107 , ASN E:109 , MG E:164 , HOH E:171 , HOH E:204	BINDING SITE FOR RESIDUE UDP E 165
12	BC3	SOFTWARE	LYS F:9 , HIS F:53 , TYR F:58 , ASN F:62 , ARG F:86 , ARG F:99 , ILE F:106 , ARG F:107 , ASN F:109 , MG F:165 , HOH F:195	BINDING SITE FOR RESIDUE UDP F 166

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

(no "Cis Peptide Bond" information available for 3EIC)

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

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_MIMIV	109-117	6	A:109-117 B:109-117 C:109-117 D:109-117 E:109-117 F:109-117

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_MIMIV	109-117	6	A:109-117 - C:109-117 - E:109-117 -

Biological Unit 2 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_MIMIV	109-117	6	- B:109-117 - D:109-117 - F:109-117

(no "Exon" information available for 3EIC)

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:133
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:133
                              1                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128   
            NDK_MIMIV     - --MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
               SCOP domains d3eica_ A: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh......hhhhhhh.......eee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------NDP_KINAS-------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eic A  -1 AGLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
                                     8        18        28        38        48        58        68        78        88        98       108       118       128

Chain B from PDB  Type:PROTEIN  Length:130
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
            NDK_MIMIV     1 MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPE 130
               SCOP domains d3eicb_ B: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeee.hhhhhhhhhhh......hhhhhhh.......eee..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------NDP_KINAS------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eic B   1 LQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPE 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain C from PDB  Type:PROTEIN  Length:132
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:132
                             1                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129  
            NDK_MIMIV     - -MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
               SCOP domains d3eicc_ C: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh......hhhhhhh.......eee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------NDP_KINAS-------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3eic C   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain D from PDB  Type:PROTEIN  Length:132
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:132
                             1                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129  
            NDK_MIMIV     - -MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
               SCOP domains d3eicd_ D: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhh...hhhhhhhhhhh..eeeeeeeeehhhhhhhhhhh......hhhhhhh.......eee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------NDP_KINAS-------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3eic D   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain E from PDB  Type:PROTEIN  Length:132
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:132
                             1                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129  
            NDK_MIMIV     - -MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
               SCOP domains d3eice_ E: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhh...hhhhhhhhhhh..eeeeeeeeehhhhhhhhhhh......hhhhhhh.......eee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------NDP_KINAS-------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3eic E   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain F from PDB  Type:PROTEIN  Length:130
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:130
                             1                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129
            NDK_MIMIV     - -MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFP 129
               SCOP domains d3eicf_ F: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhh.hhhhhhhhh....eeeeeeeeehhhhhhhhhhh......hhhhhhh.......eee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------NDP_KINAS------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eic F   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFP 129
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Legend:		→ Mismatch	(orange background)
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	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: Ferredoxin-like (1795)

Superfamily: Nucleoside diphosphate kinase, NDK (129)

Family: Nucleoside diphosphate kinase, NDK (112)

Protein domain: automated matches (46)

Acanthamoeba polyphaga mimivirus [TaxId: 212035] (23)

1a	d3eica_	A:
1b	d3eicb_	B:
1c	d3eicc_	C:
1d	d3eicd_	D:
1e	d3eice_	E:
1f	d3eicf_	F:

(no "CATH Domain" information available for 3EIC)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (NDK_MIMIV | Q5UQL3)

molecular function
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004550	nucleoside diphosphate kinase activity	Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
	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:0006241	CTP biosynthetic process	The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
	GO:0006183	GTP biosynthetic process	The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate.
	GO:0006228	UTP biosynthetic process	The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate.
	GO:0006165	nucleoside diphosphate phosphorylation	The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
	GO:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
	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.

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2b8p	X-RAY STRUCTURE OF ACANTHAMOEBA PLOYPHAGA MIMIVIRUS NUCLEOSIDE DIPHOSPHATE KINASE
2b8q	X-RAY STRUCTURE OF ACANTHAMOEBA PLOYPHAGA MIMIVIRUS NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH TDP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (0, 0)

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