2DY9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE IN COMPLEX WITH ADP

Authors :   M. Kato-Murayama, K. Murayama, T. Terada, M. Shirouzu, S. Yokoyama, Ri Structural Genomics/Proteomics Initiative (Rsgi)

Date :   08 Sep 06 (Deposition) - 08 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   Nucleoside Binding, Kinase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Kato-Murayama, K. Murayama, T. Terada, M. Shirouzu, S. Yokoyama
Crystal Structure Of Nucleoside Diphosphate Kinase In Complex With Adp
To Be Published
PubMed: search

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NDK
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3
	Synonym	:	NDK, NDP KINASE, NUCLEOSIDE-2-P KINASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CL	4	Ligand/Ion	CHLORIDE ION
3	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	ADP	3	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ADP A:501 , HOH A:732 , HOH A:735 , HOH A:774	BINDING SITE FOR RESIDUE MG A 601
2	AC2	SOFTWARE	ALA A:96 , ALA A:102 , ALA A:103	BINDING SITE FOR RESIDUE CL A 701
3	AC3	SOFTWARE	ARG A:150 , ALA A:151 , ALA A:152	BINDING SITE FOR RESIDUE CL A 702
4	AC4	SOFTWARE	GLY B:95 , ALA B:96 , ALA B:103	BINDING SITE FOR RESIDUE CL B 703
5	AC5	SOFTWARE	ARG B:150 , ALA B:151 , ALA B:152	BINDING SITE FOR RESIDUE CL B 704
6	AC6	SOFTWARE	LYS A:15 , HIS A:58 , PHE A:63 , LEU A:67 , ARG A:91 , THR A:97 , ARG A:108 , ILE A:119 , ASN A:121 , MG A:601 , HOH A:714 , HOH A:730 , HOH A:754 , HOH A:764	BINDING SITE FOR RESIDUE ADP A 501

(no "SS Bond" information available for 2DY9)

(no "Cis Peptide Bond" information available for 2DY9)

(no "SAP(SNP)/Variant" information available for 2DY9)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_PYRHO	118-126	2	A:121-129 B:121-129

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_PYRHO	118-126	6	A:121-129 B:121-129

(no "Exon" information available for 2DY9)

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:154
 aligned with NDK_PYRHO | O58429 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151    
            NDK_PYRHO     2 SETERTLVIIKPDAVVRGLIGEIISRFEKKGLKIVGMKMIWIDRELAEKHYEEHREKPFFKALIDYITKTPVVVMVLEGRYAVEVVRKMAGATDPKDAAPGTIRGDFGLEVSDAICNVIHASDSKESAEREISLFFKPEELFEYPRAADWFYKK 155
               SCOP domains d2dy9a_ A: Nucleoside diphosphate kinase, NDK                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh..........hhhhhhh..........eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dy9 A   5 SETERTLVIIKPDAVVRGLIGEIISRFEKKGLKIVGMKMIWIDRELAEKHYEEHREKPFFKALIDYITKTPVVVMVLEGRYAVEVVRKMAGATDPKDAAPGTIRGDFGLEVSDAICNVIHASDSKESAEREISLFFKPEELFEYPRAADWFYKK 158
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with NDK_PYRHO | O58429 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
            NDK_PYRHO     2 SETERTLVIIKPDAVVRGLIGEIISRFEKKGLKIVGMKMIWIDRELAEKHYEEHREKPFFKALIDYITKTPVVVMVLEGRYAVEVVRKMAGATDPKDAAPGTIRGDFGLEVSDAICNVIHASDSKESAEREISLFFKPEELFEYPRAADWFYKKGI 157
               SCOP domains d2dy9b_ B: Nucleoside diphosphate kinase, NDK                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh..........hhhhhhh..........eee..hhhhhhhhhhhhhhhhhh....hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------NDP_KINAS------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dy9 B   5 SETERTLVIIKPDAVVRGLIGEIISRFEKKGLKIVGMKMIWIDRELAEKHYEEHREKPFFKALIDYITKTPVVVMVLEGRYAVEVVRKMAGATDPKDAAPGTIRGDFGLEVSDAICNVIHASDSKESAEREISLFFKPEELFEYPRAADWFYKKGI 160
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154

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( (-)

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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)

Pyrococcus horikoshii [TaxId: 53953] (6)

1a	d2dy9a_	A:
1b	d2dy9b_	B:

(no "CATH Domain" information available for 2DY9)

(no "Pfam Domain" information available for 2DY9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NDK_PYRHO | O58429)

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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2dy9)

Biological Unit
	Complete Structure
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	2dy9
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	2.7.4.6
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	NDK_PYRHO \| O58429	:	2cwk 2dxd 2dxe 2dxf 2dya

2dya	THE SAME PROTEIN COMPLEX WITH TWO ADP MOLECULES RELATED ID: PHO001000698.3 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

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