1UFQ - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LIGAND-FREE HUMAN URIDINE-CYTIDINE KINASE 2

Authors :   N. N. Suzuki, K. Koizumi, M. Fukushima, A. Matsuda, F. Inagaki

Date :   06 Jun 03 (Deposition) - 04 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A,B,C,D  (2x)
Biol. Unit 3: A,B,C,D  (2x)

Keywords :   Alpha/Beta Mononucleotide-Binding Hold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. N. Suzuki, K. Koizumi, M. Fukushima, A. Matsuda, F. Inagaki
Structural Basis For The Specificity, Catalysis, And Regulation Of Human Uridine-Cytidine Kinase
Structure V. 12 751 2004
PubMed-ID: 15130468 | Reference-DOI: 10.1016/J.STR.2004.02.038
(for further references see the PDB file header)

Molecule 1 - URIDINE-CYTIDINE KINASE 2
	Chains	:	A, B, C, D
	EC Number	:	2.7.1.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX-6P
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-250
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	URIDINE-CYTIDINE KINASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (2x)	:	A	B	C	D
Biological Unit 3 (2x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1UFQ)

(no "Site" information available for 1UFQ)

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

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

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

(no "PROSITE Motif" information available for 1UFQ)

Asymmetric Unit (7, 28)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000367879	1a	ENSE00001445845	chr1:165796768-165797169	402	UCK2_HUMAN	1-33	33	4	A:19-33 B:19-33 C:19-33 D:19-33	15 15 15 15
1.2	ENST00000367879	2	ENSE00001656332	chr1:165859441-165859600	160	UCK2_HUMAN	34-87	54	4	A:34-87 B:34-87 (gaps) C:34-87 D:34-87	54 54 54 54
1.3	ENST00000367879	3	ENSE00000958515	chr1:165860463-165860559	97	UCK2_HUMAN	87-119	33	4	A:87-119 B:87-119 C:87-119 D:87-119	33 33 33 33
1.6c	ENST00000367879	6c	ENSE00001157917	chr1:165865427-165865569	143	UCK2_HUMAN	119-167	49	4	A:119-167 B:119-167 C:119-167 D:119-167	49 49 49 49
1.8b	ENST00000367879	8b	ENSE00001600798	chr1:165872419-165872516	98	UCK2_HUMAN	167-199	33	4	A:167-199 B:167-199 C:167-199 D:167-199 (gaps)	33 33 33 33
1.10	ENST00000367879	10	ENSE00001756761	chr1:165875158-165875206	49	UCK2_HUMAN	200-216	17	4	A:200-216 B:200-216 C:200-216 D:200-216	17 17 17 17
1.11g	ENST00000367879	11g	ENSE00001955918	chr1:165876921-165877346	426	UCK2_HUMAN	216-261	46	4	A:216-230 B:216-230 C:216-230 D:216-230	15 15 15 15

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:212
 aligned with UCK2_HUMAN | Q9BZX2 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:212
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228  
           UCK2_HUMAN    19 EPFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELILKTLKEITEGKTVQIPVYDFVSHSRKEETVTVYPADVVLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRVLRDISERGRDLEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILN 230
               SCOP domains d1ufqa_ A: Uridine-cytidine kinase 2                                                                                                                                                                                 SCOP domains
               CATH domains 1ufqA00 A:19-230 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhhh......eeeee.hhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...eee..............eee....eeeee......hhhhhh...eeeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a      Exon 1.2  PDB: A:34-87 UniProt: 34-87                 -------------------------------Exon 1.6c  PDB: A:119-167 UniProt: 119-167       --------------------------------Exon 1.10        -------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------Exon 1.3  PDB: A:87-119          -----------------------------------------------Exon 1.8b  PDB: A:167-199        ----------------Exon 1.11g      Transcript 1 (2)
                 1ufq A  19 EPFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELILKTLKEITEGKTVQIPVYDFVSHSRKEETVTVYPADVVLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRVLRDISERGRDLEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILN 230
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228

Chain B from PDB  Type:PROTEIN  Length:208
 aligned with UCK2_HUMAN | Q9BZX2 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:212
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228  
           UCK2_HUMAN    19 EPFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELILKTLKEITEGKTVQIPVYDFVSHSRKEETVTVYPADVVLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRVLRDISERGRDLEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILN 230
               SCOP domains d1ufqb_ B: Uridine-cytidine k    inase 2                                                                                                                                                                             SCOP domains
               CATH domains 1ufqB00 B:19-230 P-loop conta    ining nucleotide triphosphate hydrolases                                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhh....----....eeeee.hhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...eeeeeee....eeeeeeeee....eeeee......hhhhhh...eeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a      Exon 1.2  PDB: B:34-87 (gaps) UniProt: 34-87          -------------------------------Exon 1.6c  PDB: B:119-167 UniProt: 119-167       --------------------------------Exon 1.10        -------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------Exon 1.3  PDB: B:87-119          -----------------------------------------------Exon 1.8b  PDB: B:167-199        ----------------Exon 1.11g      Transcript 1 (2)
                 1ufq B  19 EPFLIGVSGGTASGKSSVCAKIVQLLGQN----RQKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELILKTLKEITEGKTVQIPVYDFVSHSRKEETVTVYPADVVLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRVLRDISERGRDLEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILN 230
                                    28        38        |-   |    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228  
                                                       47   52

Chain C from PDB  Type:PROTEIN  Length:212
 aligned with UCK2_HUMAN | Q9BZX2 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:212
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228  
           UCK2_HUMAN    19 EPFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELILKTLKEITEGKTVQIPVYDFVSHSRKEETVTVYPADVVLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRVLRDISERGRDLEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILN 230
               SCOP domains d1ufqc_ C: Uridine-cytidine kinase 2                                                                                                                                                                                 SCOP domains
               CATH domains 1ufqC00 C:19-230 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhhhh......eeeee.hhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...eee..ee....ee....eee....eeeee......hhhhhh...eeeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a      Exon 1.2  PDB: C:34-87 UniProt: 34-87                 -------------------------------Exon 1.6c  PDB: C:119-167 UniProt: 119-167       --------------------------------Exon 1.10        -------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------Exon 1.3  PDB: C:87-119          -----------------------------------------------Exon 1.8b  PDB: C:167-199        ----------------Exon 1.11g      Transcript 1 (2)
                 1ufq C  19 EPFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELILKTLKEITEGKTVQIPVYDFVSHSRKEETVTVYPADVVLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRVLRDISERGRDLEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILN 230
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228

Chain D from PDB  Type:PROTEIN  Length:210
 aligned with UCK2_HUMAN | Q9BZX2 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:212
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228  
           UCK2_HUMAN    19 EPFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELILKTLKEITEGKTVQIPVYDFVSHSRKEETVTVYPADVVLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRVLRDISERGRDLEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILN 230
               SCOP domains d1ufqd_ D: Uridine-cytidine kinase 2                                                                                                                                                                                 SCOP domains
               CATH domains 1ufqD00 D:19-230 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                CATH domains
           Pfam domains (1) ---PRK-1ufqD01 D:22-217                                                                                                                                                                                ------------- Pfam domains (1)
           Pfam domains (2) ---PRK-1ufqD02 D:22-217                                                                                                                                                                                ------------- Pfam domains (2)
           Pfam domains (3) ---PRK-1ufqD03 D:22-217                                                                                                                                                                                ------------- Pfam domains (3)
           Pfam domains (4) ---PRK-1ufqD04 D:22-217                                                                                                                                                                                ------------- Pfam domains (4)
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhhhh......eeeee.hhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...eeeeeee....eeeeeeeee....eeeee......hhhhhhhh.eeeeee.hhhhhhhhhhhhhhh--..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a      Exon 1.2  PDB: D:34-87 UniProt: 34-87                 -------------------------------Exon 1.6c  PDB: D:119-167 UniProt: 119-167       --------------------------------Exon 1.10        -------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------Exon 1.3  PDB: D:87-119          -----------------------------------------------Exon 1.8b  PDB: D:167-199 (gaps) ----------------Exon 1.11g      Transcript 1 (2)
                 1ufq D  19 EPFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELILKTLKEITEGKTVQIPVYDFVSHSRKEETVTVYPADVVLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRVLRDIS--GRDLEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILN 230
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168   |  |178       188       198       208       218       228  
                                                                                                                                                                                   172  |                                                       
                                                                                                                                                                                      175

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) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Phosphoribulokinase/pantothenate kinase (17)

Protein domain: Uridine-cytidine kinase 2 (6)

Human (Homo sapiens) [TaxId: 9606] (6)

1a	d1ufqa_	A:
1b	d1ufqb_	B:
1c	d1ufqc_	C:
1d	d1ufqd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Human (Homo sapiens) (413)

1a	1ufqD00	D:19-230
1b	1ufqA00	A:19-230
1c	1ufqC00	C:19-230
1d	1ufqB00	B:19-230

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: PRK (16)

Homo sapiens (Human) (8)

1a	PRK-1ufqD01	D:22-217
1b	PRK-1ufqD02	D:22-217
1c	PRK-1ufqD03	D:22-217
1d	PRK-1ufqD04	D:22-217

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (UCK2_HUMAN | Q9BZX2)

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:0019206	nucleoside kinase activity	Catalysis of the reaction: ATP + nucleoside = ADP + nucleoside monophosphate.
	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.
	GO:0004849	uridine kinase activity	Catalysis of the reaction: ATP + uridine = ADP + UMP.
biological process
	GO:0006238	CMP salvage	Any process that generates CMP, cytidine monophosphate, from derivatives of it without de novo synthesis.
	GO:0044211	CTP salvage	Any process which produces cytidine 5'-triphosphate (CTP) from derivatives of it, without de novo synthesis.
	GO:0044206	UMP salvage	Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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:0006206	pyrimidine nucleobase metabolic process	The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
	GO:0043097	pyrimidine nucleoside salvage	Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Cis Peptide Bonds
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Access by PDB/NDB ID
	1ufq
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	UCK2_HUMAN \| Q9BZX2
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	2.7.1.48
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	UCK2_HUMAN \| Q9BZX2
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UniProtKB/Swiss-Prot
	UCK2_HUMAN \| Q9BZX2	:	1udw 1uei 1uej 1uj2 1xrj

1udw	THE SAME PROTEIN COMPLEXED WITH A FEEDBACK-INHIBITOR, CTP.
1uei	THE SAME PROTEIN COMPLEXED WITH A FEEDBACK-INHIBITOR, UTP.
1uej	THE SAME PROTEIN COMPLEXED WITH A SUBSTRATE, CYTIDINE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (7, 28)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (15, 15)

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