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Title :   CRYSTAL STRUCTURE OF ACANTHAMOEBA POLYPHAGA MIMIVIRUS NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DGDP

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

Date :   28 Oct 07 (Deposition) - 04 Nov 08 (Release) - 07 Jul 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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 Protein, Atp- Binding, Kinase, Magnesium, Metal-Binding, Nucleotide Metabolism, Nucleotide-Binding, Phosphorylation (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	:	BL21 (DE3) ROSETTA PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NDK
	Organism Common	:	APMV
	Organism Scientific	:	ACANTHAMOEBA POLYPHAGA MIMIVIRUS
	Organism Taxid	:	212035
	Synonym	:	NDK, NDP KINASE

		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	DGI	6	Ligand/Ion	2'-DEOXYGUANOSINE-5'-DIPHOSPHATE
2	MG	6	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 6)

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

Biological Unit 2 (1, 6)

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

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:86 , ARG A:99	BINDING SITE FOR RESIDUE MG A 138
2	AC2	SOFTWARE	HIS B:53	BINDING SITE FOR RESIDUE MG B 138
3	AC3	SOFTWARE	ARG D:86 , ARG D:99	BINDING SITE FOR RESIDUE MG D 138
4	AC4	SOFTWARE	LYS A:9 , HIS A:53 , TYR A:58 , ASN A:62 , ARG A:86 , ARG A:99 , ILE A:106 , ARG A:107 , ASN A:109 , ASP A:115 , HOH A:181	BINDING SITE FOR RESIDUE DGI A 139
5	AC5	SOFTWARE	LYS B:9 , TYR B:50 , HIS B:53 , TYR B:58 , ARG B:86 , ARG B:99 , ILE B:106 , ARG B:107 , ASN B:109 , HIS B:112	BINDING SITE FOR RESIDUE DGI B 140
6	AC6	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 , HIS C:112 , HOH C:185	BINDING SITE FOR RESIDUE DGI C 141
7	AC7	SOFTWARE	LYS D:9 , HIS D:53 , TYR D:58 , ASN D:62 , ARG D:86 , ARG D:99 , ILE D:106 , ARG D:107 , ASN D:109	BINDING SITE FOR RESIDUE DGI D 142
8	AC8	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 , HOH E:202	BINDING SITE FOR RESIDUE DGI E 143
9	AC9	SOFTWARE	LYS F:9 , TYR F:50 , HIS F:53 , TYR F:58 , ASN F:62 , ARG F:86 , GLN F:89 , ARG F:99 , ILE F:106 , ARG F:107 , ASN F:109 , HIS F:112	BINDING SITE FOR RESIDUE DGI F 144

(no "SS Bond" information available for 3B6B)

(no "Cis Peptide Bond" information available for 3B6B)

(no "SAP(SNP)/Variant" information available for 3B6B)

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 3B6B)

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:131
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:131
                             1                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129 
            NDK_MIMIV     - -MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPE 130
               SCOP domains d3b6ba_ A: Nucleoside diphosphate kinase, NDK                                                                                       SCOP domains
               CATH domains 3b6bA00 A:0-130  [code=3.30.70.141, no name defined]                                                                                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
                 3b6b A   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPE 130
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
            NDK_MIMIV     1 MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFP 129
               SCOP domains d3b6bb_ B: Nucleoside diphosphate kinase, NDK                                                                                     SCOP domains
               CATH domains 3b6bB00 B:1-129  [code=3.30.70.141, no name defined]                                                                              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
                 3b6b B   1 LQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFP 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

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 d3b6bc_ C: Nucleoside diphosphate kinase, NDK                                                                                        SCOP domains
               CATH domains 3b6bC00 C:0-131  [code=3.30.70.141, no name defined]                                                                                 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
                 3b6b C   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain D from PDB  Type:PROTEIN  Length:131
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:131
                             1                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129 
            NDK_MIMIV     - -MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPE 130
               SCOP domains d3b6bd_ D: Nucleoside diphosphate kinase, NDK                                                                                       SCOP domains
               CATH domains 3b6bD00 D:0-130  [code=3.30.70.141, no name defined]                                                                                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
                 3b6b D   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPE 130
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain E from PDB  Type:PROTEIN  Length:131
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:131
                             1                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129 
            NDK_MIMIV     - -MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPE 130
               SCOP domains d3b6be_ E: Nucleoside diphosphate kinase, NDK                                                                                       SCOP domains
               CATH domains 3b6bE00 E:0-130  [code=3.30.70.141, no name defined]                                                                                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
                 3b6b E   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPE 130
                                     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 d3b6bf_ F: Nucleoside diphosphate kinase, NDK                                                                                      SCOP domains
               CATH domains 3b6bF00 F:0-129  [code=3.30.70.141, no name defined]                                                                               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
                 3b6b F   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFP 129
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

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(

)

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: Nucleoside diphosphate kinase, NDK (66)

Acanthamoeba polyphaga mimivirus [TaxId: 212035] (1)

1a	d3b6ba_	A:
1b	d3b6bb_	B:
1c	d3b6bc_	C:
1d	d3b6bd_	D:
1e	d3b6be_	E:
1f	d3b6bf_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.141, no name defined] (46)

Apmv (Acanthamoeba polyphaga mimivirus) (1)

1a	3b6bC00	C:0-131
1b	3b6bA00	A:0-130
1c	3b6bD00	D:0-130
1d	3b6bE00	E:0-130
1e	3b6bF00	F:0-129
1f	3b6bB00	B:1-129

(no "Pfam Domain" information available for 3B6B)

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	CRYSTAL STRUCTURE OF ACANTHAMOEBA POLYPHAGA MIMIVIRUS NDK, THE FIRST VIRAL NUCLEOSIDE DIPHOSPHATE KINASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (9, 9)

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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SCOP Domains (1, 6)

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