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Title :   CRYSTAL STRUCTURE OF THE MIMIVIRUS NDK N62L MUTANT COMPLEXED WITH UDP

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

Date :   23 Nov 08 (Deposition) - 11 Aug 09 (Release) - 11 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   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	:	MIMI_R418, NDK
	Mutation	:	YES
	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:138 , HOH A:272	BINDING SITE FOR RESIDUE MG A 160
02	AC2	SOFTWARE	LYS A:9 , HIS A:53 , TYR A:58 , LEU A:62 , ARG A:86 , ARG A:99 , ILE A:106 , ARG A:107 , ASN A:109 , MG A:160 , HOH A:226 , HOH A:238 , HOH A:272 , HOH A:300	BINDING SITE FOR RESIDUE UDP A 138
03	AC3	SOFTWARE	UDP B:138 , HOH B:301	BINDING SITE FOR RESIDUE MG B 161
04	AC4	SOFTWARE	LYS B:9 , HIS B:53 , TYR B:58 , LEU B:62 , ARG B:86 , ARG B:99 , ILE B:106 , ARG B:107 , ASN B:109 , HOH B:145 , MG B:161 , HOH B:301	BINDING SITE FOR RESIDUE UDP B 138
05	AC5	SOFTWARE	UDP C:138 , HOH C:264	BINDING SITE FOR RESIDUE MG C 162
06	AC6	SOFTWARE	LYS C:9 , HIS C:53 , TYR C:58 , LEU C:62 , ARG C:86 , ARG C:99 , ILE C:106 , ARG C:107 , ASN C:109 , MG C:162 , HOH C:163 , HOH C:270	BINDING SITE FOR RESIDUE UDP C 138
07	AC7	SOFTWARE	ASP D:115 , UDP D:138 , HOH D:263	BINDING SITE FOR RESIDUE MG D 163
08	AC8	SOFTWARE	LYS D:9 , HIS D:53 , TYR D:58 , LEU D:62 , ARG D:86 , ARG D:99 , ILE D:106 , ARG D:107 , ASN D:109 , HOH D:154 , MG D:163 , HOH D:259 , HOH D:263	BINDING SITE FOR RESIDUE UDP D 138
09	AC9	SOFTWARE	ARG E:86 , ASP E:115 , UDP E:138	BINDING SITE FOR RESIDUE MG E 164
10	BC1	SOFTWARE	LYS E:9 , HIS E:53 , TYR E:58 , LEU E:62 , ARG E:86 , ARG E:99 , ILE E:106 , ARG E:107 , ASN E:109 , HOH E:147 , MG E:164	BINDING SITE FOR RESIDUE UDP E 138
11	BC2	SOFTWARE	ASP F:115 , UDP F:138	BINDING SITE FOR RESIDUE MG F 165
12	BC3	SOFTWARE	LYS F:9 , HIS F:53 , TYR F:58 , LEU F:62 , ARG F:86 , ARG F:99 , ILE F:106 , ARG F:107 , ASN F:109 , MG F:165 , HOH F:269	BINDING SITE FOR RESIDUE UDP F 138

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

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

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

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 3FCW)

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 d3fcwa_ 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
                 3fcw A   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDLCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPE 130
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:128
                                    10        20        30        40        50        60        70        80        90       100       110       120        
            NDK_MIMIV     1 MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWF 128
               SCOP domains d3fcwb_ 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
                 3fcw B   1 LQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDLCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWF 128
                                    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 d3fcwc_ 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
                 3fcw C   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDLCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 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 d3fcwd_ 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
                 3fcw D   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDLCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPE 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 d3fcwe_ E: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh......hhhhhhh.......eee..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------NDP_KINAS------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fcw E   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDLCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPE 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 d3fcwf_ F: 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
                 3fcw F   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDLCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFP 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: automated matches (46)

Acanthamoeba polyphaga mimivirus [TaxId: 212035] (23)

1a	d3fcwa_	A:
1b	d3fcwb_	B:
1c	d3fcwc_	C:
1d	d3fcwd_	D:
1e	d3fcwe_	E:
1f	d3fcwf_	F:

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

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

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 THE MIMIVIRUS NDK

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

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PROSITE Motifs (1, 6)

Exons (0, 0)

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SCOP Domains (1, 6)

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