1NSQ - JenaLib

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Title :   MECHANISM OF PHOSPHATE TRANSFER BY NUCLEOSIDE DIPHOSPHATE KINASE: X-RAY STRUCTURES OF A PHOSPHO-HISTIDINE INTERMEDIATE OF THE ENZYMES FROM DROSOPHILA AND DICTYOSTELIUM

Authors :   J. Janin, M. Chiadmi, S. Morera, G. Lebras, I. Lascu

Date :   24 Apr 95 (Deposition) - 10 Jul 95 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.18

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

Keywords :   Phosphotransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Morera, M. Chiadmi, G. Lebras, I. Lascu, J. Janin
Mechanism Of Phosphate Transfer By Nucleoside Diphosphate Kinase: X-Ray Structures Of The Phosphohistidine Intermediate Of The Enzymes From Drosophila And Dictyostelium.
Biochemistry V. 34 11062 1995
PubMed-ID: 7669763 | Reference-DOI: 10.1021/BI00035A011
(for further references see the PDB file header)

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
	Chains	:	A, B, C
	EC Number	:	2.7.4.6
	Engineered	:	YES
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	HIP	3	Mod. Amino Acid	ND1-PHOSPHONOHISTIDINE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	HIP	6	Mod. Amino Acid	ND1-PHOSPHONOHISTIDINE

(no "Site" information available for 1NSQ)

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

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

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDKA_DROME	116-124	3	A:116-124 B:116-124 C:116-124

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.	NDKA_DROME	116-124	6	A:116-124 B:116-124 C:116-124

(no "Exon" information available for 1NSQ)

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
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Chain A from PDB  Type:PROTEIN  Length:152
 aligned with NDKA_DROME | P08879 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           NDKA_DROME     2 AANKERTFIMVKPDGVQRGLVGKIIERFEQKGFKLVALKFTWASKELLEKHYADLSARPFFPGLVNYMNSGPVVPMVWEGLNVVKTGRQMLGATNPADSLPGTIRGDFCIQVGRNIIHGSDAVESAEKEIALWFNEKELVTWTPAAKDWIYE 153
               SCOP domains d1nsqa_ A: Nucleoside diphosphate kinase, NDK                                                                                                            SCOP domains
               CATH domains 1nsqA00 A:2-153  [code=3.30.70.141, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.hhhhh...hhhhhhhhhhh..eeeee......hhhhhhh.hhh.....hhhhhhhh.....eeeeee...hhhhhhhhh....hhhhhh..hhhhh........eee...hhhhhhhhhhh..hhh........hhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nsq A   2 AANKERTFIMVKPDGVQRGLVGKIIERFEQKGFKLVALKFTWASKELLEKHYADLSARPFFPGLVNYMNSGPVVPMVWEGLNVVKTGRQMLGATNPADSLPGTIRGDFCIQVGRNIIhGSDAVESAEKEIALWFNEKELVTWTPAAKDWIYE 153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
                                                                                                                                               119-HIP

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with NDKA_DROME | P08879 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           NDKA_DROME     2 AANKERTFIMVKPDGVQRGLVGKIIERFEQKGFKLVALKFTWASKELLEKHYADLSARPFFPGLVNYMNSGPVVPMVWEGLNVVKTGRQMLGATNPADSLPGTIRGDFCIQVGRNIIHGSDAVESAEKEIALWFNEKELVTWTPAAKDWIYE 153
               SCOP domains d1nsqb_ B: Nucleoside diphosphate kinase, NDK                                                                                                            SCOP domains
               CATH domains 1nsqB00 B:2-153  [code=3.30.70.141, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nsq B   2 AANKERTFIMVKPDGVQRGLVGKIIERFEQKGFKLVALKFTWASKELLEKHYADLSARPFFPGLVNYMNSGPVVPMVWEGLNVVKTGRQMLGATNPADSLPGTIRGDFCIQVGRNIIhGSDAVESAEKEIALWFNEKELVTWTPAAKDWIYE 153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
                                                                                                                                               119-HIP

Chain C from PDB  Type:PROTEIN  Length:152
 aligned with NDKA_DROME | P08879 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           NDKA_DROME     2 AANKERTFIMVKPDGVQRGLVGKIIERFEQKGFKLVALKFTWASKELLEKHYADLSARPFFPGLVNYMNSGPVVPMVWEGLNVVKTGRQMLGATNPADSLPGTIRGDFCIQVGRNIIHGSDAVESAEKEIALWFNEKELVTWTPAAKDWIYE 153
               SCOP domains d1nsqc_ C: Nucleoside diphosphate kinase, NDK                                                                                                            SCOP domains
               CATH domains 1nsqC00 C:2-153  [code=3.30.70.141, no name defined]                                                                                                     CATH domains
           Pfam domains (1) ----NDK-1nsqC01 C:6-140                                                                                                                    ------------- Pfam domains (1)
           Pfam domains (2) ----NDK-1nsqC02 C:6-140                                                                                                                    ------------- Pfam domains (2)
           Pfam domains (3) ----NDK-1nsqC03 C:6-140                                                                                                                    ------------- Pfam domains (3)
         Sec.struct. author ........................................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nsq C   2 AANKERTFIMVKPDGVQRGLVGKIIERFEQKGFKLVALKFTWASKELLEKHYADLSARPFFPGLVNYMNSGPVVPMVWEGLNVVKTGRQMLGATNPADSLPGTIRGDFCIQVGRNIIhGSDAVESAEKEIALWFNEKELVTWTPAAKDWIYE 153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
                                                                                                                                               119-HIP

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)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (2)

1a	d1nsqa_	A:
1b	d1nsqb_	B:
1c	d1nsqc_	C:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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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)

Fruit fly (Drosophila melanogaster) (2)

1a	1nsqA00	A:2-153
1b	1nsqB00	B:2-153
1c	1nsqC00	C:2-153

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: no clan defined [family: NDK] (40)

Family: NDK (40)

Drosophila melanogaster (Fruit fly) (2)

1a	NDK-1nsqC01	C:6-140
1b	NDK-1nsqC02	C:6-140
1c	NDK-1nsqC03	C:6-140

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (NDKA_DROME | P08879)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	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:0034332	adherens junction organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
	GO:0007427	epithelial cell migration, open tracheal system	The orderly movement of epithelial cells during development of an open tracheal system. An example of this is found in Drosophila melanogaster.
	GO:0016334	establishment or maintenance of polarity of follicular epithelium	Any cellular process that results in the specification, formation or maintenance of a polarized follicular epithelial sheet.
	GO:0007017	microtubule-based process	Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
	GO:0006165	nucleoside diphosphate phosphorylation	The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
	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:0007424	open tracheal system development	The process whose specific outcome is the progression of an open tracheal system over time, from its formation to the mature structure. An open tracheal system is a respiratory system, a branched network of epithelial tubes that supplies oxygen to target tissues via spiracles. An example of this is found in Drosophila melanogaster.
	GO:0018105	peptidyl-serine phosphorylation	The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
	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:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	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:0035152	regulation of tube architecture, open tracheal system	Ensuring that tracheal cells form and maintain tubular structures with the correct size and shape for their position in the network. This is essential for efficient flow of gases through the tracheal network.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005874	microtubule	Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
	GO:0005875	microtubule associated complex	Any multimeric complex connected to a microtubule.
	GO:0005880	nuclear microtubule	Any microtubule in the nucleus of a cell.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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