2QSY - JenaLib

Title :   HUMAN NICOTINAMIDE RIBOSIDE KINASE 1 IN COMPLEX WITH ADP

Authors :   W. M. Rabeh, W. Tempel, L. Nedyalkova, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, C. Brenner, H. Park, Structural Genomics Consortium (Sgc)

Date :   31 Jul 07 (Deposition) - 14 Aug 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A

Keywords :   Non-Protein Kinase, Nad+, Nicotinamide Riboside, Nrk1, Nicotinamide Riboside Kinase Activity, Nicotinic Acid Riboside Kinase Activity, Nad Biosynthesis, Adp, Structural Genomics, Structural Genomics Consortium, Sgc, Alternative Splicing, Atp-Binding, Nucleotide-Binding, Pyridine Nucleotide Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Tempel, W. M. Rabeh, K. L. Bogan, P. Belenky, M. Wojcik, H. F. Seidle, L. Nedyalkova, T. Yang, A. A. Sauve, H. W. Park, C. Brenner
Nicotinamide Riboside Kinase Structures Reveal New Pathways To Nad(+).
Plos Biol. V. 5 E263 2007
PubMed-ID: 17914902 | Reference-DOI: 10.1371/JOURNAL.PBIO.0050263
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:17 , ADP A:1101 , HOH A:1108 , HOH A:1109 , HOH A:1110 , HOH A:1173	BINDING SITE FOR RESIDUE MG A 1102
2	AC2	SOFTWARE	ASN A:13 , SER A:14 , GLY A:15 , LYS A:16 , THR A:17 , THR A:18 , ARG A:128 , ARG A:132 , LYS A:172 , SER A:173 , GLU A:174 , LEU A:177 , MG A:1102 , HOH A:1108 , HOH A:1109 , HOH A:1110 , HOH A:1148	BINDING SITE FOR RESIDUE ADP A 1101
3	AC3	SOFTWARE	LEU A:19 , ASN A:22 , GLU A:174	BINDING SITE FOR RESIDUE UNX A 1103
4	AC4	SOFTWARE	LEU A:53	BINDING SITE FOR RESIDUE UNX A 1104
5	AC5	SOFTWARE	LEU A:58 , LEU A:61	BINDING SITE FOR RESIDUE UNX A 1105
6	AC6	SOFTWARE	ASP A:109 , TRP A:112	BINDING SITE FOR RESIDUE UNX A 1106
7	AC7	SOFTWARE	LEU A:168 , ASP A:169 , LYS A:172 , GLN A:180	BINDING SITE FOR RESIDUE UNX A 1107

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (7, 7)

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000361092	1b	ENSE00001849826	chr9:77703125-77702924	202	NRK1_HUMAN	-	0	0	-	-
1.3a	ENST00000361092	3a	ENSE00002164399	chr9:77698066-77698003	64	NRK1_HUMAN	1-10	10	1	A:1-10	10
1.5	ENST00000361092	5	ENSE00000803844	chr9:77692496-77692406	91	NRK1_HUMAN	10-40	31	1	A:10-40	31
1.6	ENST00000361092	6	ENSE00000707162	chr9:77692123-77692075	49	NRK1_HUMAN	41-57	17	1	A:41-57	17
1.7a	ENST00000361092	7a	ENSE00000707131	chr9:77684958-77684811	148	NRK1_HUMAN	57-106	50	1	A:57-106 (gaps)	50
1.7c	ENST00000361092	7c	ENSE00000707111	chr9:77684729-77684658	72	NRK1_HUMAN	106-130	25	1	A:106-130	25
1.7d	ENST00000361092	7d	ENSE00000707110	chr9:77684018-77683912	107	NRK1_HUMAN	130-166	37	1	A:130-166	37
1.8b	ENST00000361092	8b	ENSE00001391026	chr9:77681756-77681673	84	NRK1_HUMAN	166-194	29	1	A:166-189	24
1.9b	ENST00000361092	9b	ENSE00001843408	chr9:77676483-77676116	368	NRK1_HUMAN	194-199	6	0	-	-

Sequences/Alignments

Asymmetric/Biological 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:180
 aligned with NRK1_HUMAN | Q9NWW6 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
           NRK1_HUMAN     1 MKTFIIGISGVTNSGKTTLAKNLQKHLPNCSVISQDDFFKPESEIETDKNGFLQYDVLEALNMEKMMSAISCWMESARHSVVSTDQESAEEIPILIIEGFLLFNYKPLDTIWNRSYFLTIPYEECKRRRSTRVYQPPDSPGYFDGHVWPMYLKYRQEMQDITWEVVYLDGTKSEEDLFLQVYEDLIQEL 189
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qsyA00 A:1-189 P-loop containing nucleotide triphosphate hydrolases                                                                                                                          CATH domains
               Pfam domains ----AAA_17-2qsyA01 A:5-189                                                                                                                                                                    Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhh..eeeee.hhhh.hhhhh...........hhhhhhhhhhhhhhhhhhhhhh....---------..eeeee......hhhhh....eeeeee.hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a ------------------------------Exon 1.6         ------------------------------------------------Exon 1.7c  PDB: A:106-130-----------------------------------Exon 1.8b  PDB: A:166-18 Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.5  PDB: A:10-40         ----------------Exon 1.7a  PDB: A:57-106 (gaps) UniProt: 57-106   -----------------------Exon 1.7d  PDB: A:130-166            ----------------------- Transcript 1 (2)
                 2qsy A   1 SKTFIIGISGVTNSGKTTLAKNLQKHLPNCSVISQDDFFKPESEIETDKNGFLQYDVLEALNmEKmmSAISCWmESARHSVV---------IPILIIEGFLLFNYKPLDTIWNRSYFLTIPYEECKRRRSTRVYQPPDSPGYFDGHVWPmYLKYRQEmQDITWEVVYLDGTKSEEDLFLQVYEDLIQEL 189
                                    10        20        30        40        50        60  |  || 70   |    80 |       - |     100       110       120       130       140       150       160       170       180         
                                                                                         63-MSE     74-MSE  82        92                                                       150-MSE 158-MSE                           
                                                                                            66-MSE                                                                                                                       
                                                                                             67-MSE

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NRK1_HUMAN | Q9NWW6)

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: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:0050262	ribosylnicotinamide kinase activity	Catalysis of the reaction: N-ribosylnicotinamide + ATP = ADP + 2 H(+) + nicotinamide mononucleotide.
	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:0009435	NAD biosynthetic process	The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
	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:0019363	pyridine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		UNX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gln A:135 - Pro A:136	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2qsy
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	NRK1_HUMAN \| Q9NWW6
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.1.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description