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Title :   HUMAN NUCLEOSIDE DIPHOSPHATE KINASE 4

Authors :   L. Milon, P. Meyer, M. Chiadmi, A. Munier, M. Johansson, A. Karlsson, I. J. Capeau, J. Janin, M. -L. Lacombe

Date :   23 Feb 00 (Deposition) - 17 May 00 (Release) - 01 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Nucleoside Diphosphate Kinase, Nm23, Mitochondrial, Killer-Of-Prune, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Milon, P. Meyer, M. Chiadmi, A. Munier, M. Johansson, A. Karlsson, I. Lascu, J. Capeau, J. Janin, M. L. Lacombe
The Human Nm23-H4 Gene Product Is A Mitochondrial Nucleosid Diphosphate Kinase.
J. Biol. Chem. V. 275 14264 2000
PubMed-ID: 10799505 | Reference-DOI: 10.1074/JBC.275.19.14264

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PLASMID PET-28A(+) NOVAGEN
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	N-TERMINUS TRUNCATED, N-TERMINAL HIS TAG
	Synonym	:	NDPK H4

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 9)

No.	Name	Count	Type	Full Name
1	SO4	9	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:111 , ILE A:112 , SER A:113 , ARG A:114 , HOH A:507 , HOH A:510 , PRO B:59 , PHE B:60 , PRO B:62	BINDING SITE FOR RESIDUE SO4 A 160
2	AC2	SOFTWARE	ARG B:88 , THR B:94 , ARG B:105 , HOH B:519 , HOH B:528	BINDING SITE FOR RESIDUE SO4 B 163
3	AC3	SOFTWARE	ARG A:88 , THR A:94 , ARG A:105 , HOH A:525	BINDING SITE FOR RESIDUE SO4 A 164

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

(no "Cis Peptide Bond" information available for 1EHW)

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDKM_HUMAN	148-156	2	A:115-123 B:115-123

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.	NDKM_HUMAN	148-156	6	A:115-123 B:115-123

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2d	ENST00000219479	2d	ENSE00001529864	chr16:447209-447313	105	NDKM_HUMAN	1-31	31	2	A:0-2 B:1-2	3 2
1.4e	ENST00000219479	4e	ENSE00001757263	chr16:448990-449123	134	NDKM_HUMAN	31-75	45	2	A:3-42 B:3-42	40 40
1.4i	ENST00000219479	4i	ENSE00001687205	chr16:449379-449480	102	NDKM_HUMAN	76-109	34	2	A:43-76 B:43-76	34 34
1.4j	ENST00000219479	4j	ENSE00001710387	chr16:449627-449739	113	NDKM_HUMAN	110-147	38	2	A:77-114 B:77-114	38 38
1.5j	ENST00000219479	5j	ENSE00001958819	chr16:450219-450759	541	NDKM_HUMAN	147-187	41	2	A:114-142 B:114-142	29 29

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:143
 aligned with NDKM_HUMAN | O00746 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:149
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166         
           NDKM_HUMAN    27 RHGSGGPSWTRERTLVAVKPDGVQRRLVGDVIQRFERRGFTLVGMKMLQAPESVLAEHYQDLRRKPFYPALIRYMSSGPVVAMVWEGYNVVRASRAMIGHTDSAEAAPGTIRGDFSVHISRNVIHASDSVEGAQREIQLWFQSSELVSW 175
               SCOP domains d1e      hwa_ A: Nucleoside diphosphate kinase, NDK                                                                                                   SCOP domains
               CATH domains 1eh      wA00 A:0-142  [code=3.30.70.141, no name defined]                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hh------hh.eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------NDP_KINAS------------------- PROSITE
           Transcript 1 (1) 1.2d --------------------------------------------Exon 1.4i  PDB: A:43-76           Exon 1.4j  PDB: A:77-114              ---------------------------- Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.4e  PDB: A:3-42 UniProt: 31-75        -----------------------------------------------------------------------Exon 1.5j  PDB: A:114-142     Transcript 1 (2)
                 1ehw A   0 HMG------TRERTLVAVKPDGVQRRLVGDVIQRFERRGFTLVGMKMLQAPESVLAEHYQDLRRKPFYPALIRYMSSGPVVAMVWEGYNVVRASRAMIGHTDSAEAAPGTIRGDFSVHISRNVIHASDSVEGAQREIQLWFQSSELVSW 142
                              |      3        13        23        33        43        53        63        73        83        93       103       113       123       133         
                              2      3

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with NDKM_HUMAN | O00746 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
           NDKM_HUMAN     1 MGGLFWRSALRGLRCGPRAPGPSLLVRHGSGGPSWTRERTLVAVKPDGVQRRLVGDVIQRFERRGFTLVGMKMLQAPESVLAEHYQDLRRKPFYPALIRYMSSGPVVAMVWEGYNVVRASRAMIGHTDSAEAAPGTIRGDFSVHISRNVIHASDSVEGAQREIQLWFQSSELVSW 175
               SCOP domains d1                                 ehwb_ B: Nucleoside diphosphate kinase, NDK                                                                                                  SCOP domains
               CATH domains 1e                                 hwB00 B:1-142  [code=3.30.70.141, no name defined]                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---------------------------------...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------NDP_KINAS------------------- PROSITE
           Transcript 1 (1) Exon 1.2d  PDB: B:1-2          --------------------------------------------Exon 1.4i  PDB: B:43-76           Exon 1.4j  PDB: B:77-114              ---------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.4e  PDB: B:3-42 UniProt: 31-75        -----------------------------------------------------------------------Exon 1.5j  PDB: B:114-142     Transcript 1 (2)
                 1ehw B   1 MG---------------------------------TRERTLVAVKPDGVQRRLVGDVIQRFERRGFTLVGMKMLQAPESVLAEHYQDLRRKPFYPALIRYMSSGPVVAMVWEGYNVVRASRAMIGHTDSAEAAPGTIRGDFSVHISRNVIHASDSVEGAQREIQLWFQSSELVSW 142
                             |       -         -         -     |   7        17        27        37        47        57        67        77        87        97       107       117       127       137     
                             2                                 3

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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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)

Human (Homo sapiens), NDK4 [TaxId: 9606] (1)

1a	d1ehwa_	A:
1b	d1ehwb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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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)

Human (Homo sapiens) (5)

1a	1ehwA00	A:0-142
1b	1ehwB00	B:1-142

(no "Pfam Domain" information available for 1EHW)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NDKM_HUMAN | O00746)

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:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0006869	lipid transport	The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0015949	nucleobase-containing small molecule interconversion	The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
	GO:0006165	nucleoside diphosphate phosphorylation	The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
	GO:0009116	nucleoside metabolic process	The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
	GO:0009142	nucleoside triphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
	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.
	GO:0006163	purine nucleotide metabolic process	The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0006220	pyrimidine nucleotide metabolic process	The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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Ligands, Modified Residues, Ions (1, 3)

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