1BE4 - JenaLib

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Title :   NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM B FROM BOVINE RETINA

Authors :   J. E. Ladner, N. G. Abdulaev, D. L. Kakuev, G. N. Karaschuk, M. Tordova, E. Eisenstein, J. H. Fujiwara, K. D. Ridge, G. L. Gilliland

Date :   19 May 98 (Deposition) - 13 Jan 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

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

Reference :   N. G. Abdulaev, G. N. Karaschuk, J. E. Ladner, D. L. Kakuev, A. V. Yakhyaev, M. Tordova, I. O. Gaidarov, V. I. Popov, J. H. Fujiwara, D. Chinchilla, E. Eisenstein, G. L. Gilliland, K. D. Ridge
Nucleoside Diphosphate Kinase From Bovine Retina: Purification, Subcellular Localization, Molecular Cloning, And Three-Dimensional Structure.
Biochemistry V. 37 13958 1998
PubMed-ID: 9760230 | Reference-DOI: 10.1021/BI980853S

Molecule 1 - NUCLEOSIDE DIPHOSPHATE TRANSFERASE
	Chains	:	A, B, C
	EC Number	:	2.7.4.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organ	:	EYE
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Tissue	:	RETINA

		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	PCG	3	Ligand/Ion	CYCLIC GUANOSINE MONOPHOSPHATE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	PCG	6	Ligand/Ion	CYCLIC GUANOSINE MONOPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:12 , TYR A:52 , PHE A:60 , THR A:94 , GLY A:113 , ASN A:115 , HIS A:118 , HOH A:300 , HOH A:394 , GLU B:152	BINDING SITE FOR RESIDUE PCG A 160
2	AC2	SOFTWARE	LYS B:12 , TYR B:52 , PHE B:60 , ARG B:88 , THR B:94 , VAL B:112 , ASN B:115 , HIS B:118 , HOH B:278 , GLU C:152	BINDING SITE FOR RESIDUE PCG B 160
3	AC3	SOFTWARE	GLU A:152 , LYS C:12 , TYR C:52 , PHE C:60 , LEU C:64 , THR C:94 , VAL C:112 , ASN C:115 , HIS C:118 , HOH C:304 , HOH C:332 , HOH C:401 , HOH C:443	BINDING SITE FOR RESIDUE PCG C 160
4	NUL	UNKNOWN	LYS A:12 , TYR A:52 , VAL A:112 , ASN A:115 , HIS A:118 , GLU A:152	C-GMP BINDING SITE.

(no "SS Bond" information available for 1BE4)

(no "Cis Peptide Bond" information available for 1BE4)

(no "SAP(SNP)/Variant" information available for 1BE4)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDKA2_BOVIN	115-123	3	A:115-123 B:115-123 C: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.	NDKA2_BOVIN	115-123	6	A:115-123 B:115-123 C:115-123

(no "Exon" information available for 1BE4)

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:151
 aligned with NDKA2_BOVIN | P52175 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 
          NDKA2_BOVIN     2 ANSERTFIAIKPDGVQRGLMGEIIKRFEQKGFRLVAMKFMRASEDLLKEHYIDLKDRPFFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIALWFRPEELVNYKSCAQNWIYE 152
               SCOP domains d1be4a_ A: Nucleoside diphosphate kinase, NDK                                                                                                           SCOP domains
               CATH domains 1be4A00 A:2-152  [code=3.30.70.141, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.hhhhh...hhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhh.....hhhhhhhhh..eeeeeeee...hhhhhhhhh....hhh.....hhhhh........eee...hhhhhhhhhhh..hhh........hhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1be4 A   2 ANSERTFIAIKPDGVQRGLMGEIIKRFEQKGFRLVAMKFMRASEDLLKEHYIDLKDRPFFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIALWFRPEELVNYKSCAQNWIYE 152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with NDKA2_BOVIN | P52175 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 
          NDKA2_BOVIN     2 ANSERTFIAIKPDGVQRGLMGEIIKRFEQKGFRLVAMKFMRASEDLLKEHYIDLKDRPFFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIALWFRPEELVNYKSCAQNWIYE 152
               SCOP domains d1be4b_ B: Nucleoside diphosphate kinase, NDK                                                                                                           SCOP domains
               CATH domains 1be4B00 B:2-152  [code=3.30.70.141, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.hhhhhh..hhhhhhhhhhh..eeeeeeee...hhhhhhh..hhh..hhhhhhhhhh....eeeeeee...hhhhhhhhh....hhh.....hhhhh...hhh..eee...hhhhhhhhhhh.............hhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1be4 B   2 ANSERTFIAIKPDGVQRGLMGEIIKRFEQKGFRLVAMKFMRASEDLLKEHYIDLKDRPFFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIALWFRPEELVNYKSCAQNWIYE 152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with NDKA2_BOVIN | P52175 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 
          NDKA2_BOVIN     2 ANSERTFIAIKPDGVQRGLMGEIIKRFEQKGFRLVAMKFMRASEDLLKEHYIDLKDRPFFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIALWFRPEELVNYKSCAQNWIYE 152
               SCOP domains d1be4c_ C: Nucleoside diphosphate kinase, NDK                                                                                                           SCOP domains
               CATH domains 1be4C00 C:2-152  [code=3.30.70.141, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.hhhhhh..hhhhhhhhhhh..eeeeeeee...hhhhhhh.hhh....hhhhhhhhhh...eeeeeee...hhhhhhhhh....hhh.....hhhhh........eee...hhhhhhhhhhh..hhh.......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1be4 C   2 ANSERTFIAIKPDGVQRGLMGEIIKRFEQKGFRLVAMKFMRASEDLLKEHYIDLKDRPFFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIALWFRPEELVNYKSCAQNWIYE 152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

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(

)

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)

Cow (Bos taurus) [TaxId: 9913] (2)

1a	d1be4a_	A:
1b	d1be4b_	B:
1c	d1be4c_	C:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

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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)

Cattle (Bos taurus) (2)

1a	1be4A00	A:2-152
1b	1be4B00	B:2-152
1c	1be4C00	C:2-152

(no "Pfam Domain" information available for 1BE4)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (NDKA2_BOVIN | P52175)

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:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	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.

Asymmetric Unit
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Ligands, Modified Residues, Ions (1, 3)

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