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(-) Description

Title :  HUMAN NICOTINAMIDE RIBOSIDE KINASE 1 IN COMPLEX WITH NICOTINAMIDE RIBOSIDE AND AN ATP ANALOGUE
 
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 :  1.92
Chains :  Asym./Biol. Unit :  A
Keywords :  Non-Protein Kinase, Nad+, Nicotinamide Riboside, Nrk1, Nicotinamide Riboside Kinase Activity, Nicotinic Acid Riboside Kinase Activity, Nad Biosynthesis, Pyridine Nucleotide Biosynthesis, Atp Analogue, Structural Genomics, Structural Genomics Consortium, Sgc, Alternative Splicing, Atp-Binding, Nucleotide-Binding, 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

Molecule 1 - NICOTINAMIDE RIBOSIDE KINASE 1
    Chains: A
    EC Number: 2.7.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P28A-LIC
    Expression System Strain: BL21(DE3) CODON PLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NRK1, C9ORF95
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
4NNR1Ligand/IonNICOTINAMIDE RIBOSIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:17 , ASP A:36 , HOH A:231 , HOH A:232 , ANP A:1102BINDING SITE FOR RESIDUE MG A 1001
2AC2SOFTWARETHR A:12 , ASN A:13 , SER A:14 , GLY A:15 , LYS A:16 , THR A:17 , THR A:18 , ASP A:36 , ARG A:128 , ARG A:132 , TYR A:134 , LYS A:172 , SER A:173 , GLU A:174 , LEU A:177 , HOH A:231 , HOH A:232 , MG A:1001 , NNR A:1103BINDING SITE FOR RESIDUE ANP A 1102
3AC3SOFTWARETHR A:12 , ASP A:36 , PHE A:39 , TYR A:55 , ASP A:56 , ARG A:129 , TYR A:134 , GLN A:135 , HOH A:208 , ANP A:1102BINDING SITE FOR RESIDUE NNR A 1103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QT0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:135 -Pro A:136

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QT0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QT0)

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003610921bENSE00001849826chr9:77703125-77702924202NRK1_HUMAN-00--
1.3aENST000003610923aENSE00002164399chr9:77698066-7769800364NRK1_HUMAN1-10101A:1-1010
1.5ENST000003610925ENSE00000803844chr9:77692496-7769240691NRK1_HUMAN10-40311A:10-4031
1.6ENST000003610926ENSE00000707162chr9:77692123-7769207549NRK1_HUMAN41-57171A:41-5717
1.7aENST000003610927aENSE00000707131chr9:77684958-77684811148NRK1_HUMAN57-106501A:57-106 (gaps)50
1.7cENST000003610927cENSE00000707111chr9:77684729-7768465872NRK1_HUMAN106-130251A:106-13025
1.7dENST000003610927dENSE00000707110chr9:77684018-77683912107NRK1_HUMAN130-166371A:130-16637
1.8bENST000003610928bENSE00001391026chr9:77681756-7768167384NRK1_HUMAN166-194291A:166-18722
1.9bENST000003610929bENSE00001843408chr9:77676483-77676116368NRK1_HUMAN194-19960--

(-) 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:179
 aligned with NRK1_HUMAN | Q9NWW6 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:189
                              1                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178         
           NRK1_HUMAN     - --MKTFIIGISGVTNSGKTTLAKNLQKHLPNCSVISQDDFFKPESEIETDKNGFLQYDVLEALNMEKMMSAISCWMESARHSVVSTDQESAEEIPILIIEGFLLFNYKPLDTIWNRSYFLTIPYEECKRRRSTRVYQPPDSPGYFDGHVWPMYLKYRQEMQDITWEVVYLDGTKSEEDLFLQVYEDLIQ 187
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qt0A00 A:-1-187 P-loop containing nucleotide triphosphate hydrolases                                                                                                                         CATH domains
               Pfam domains ------AAA_17-2qt0A01 A:5-187                                                                                                                                                                  Pfam domains
         Sec.struct. author .....eeeeeee....hhhhhhhhhhhhh..eeeee.hhhh.hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh----------..eeeee......hhhhh....eeeeee.hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhh 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 [INCOMPLETE] 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)
                 2qt0 A  -1 RGSKTFIIGISGVTNSGKTTLAKNLQKHLPNCSVISQDDFFKPESEIETDKNGFLQYDVLEALNmEKmmSAISCWmESARHSV----------IPILIIEGFLLFNYKPLDTIWNRSYFLTIPYEECKRRRSTRVYQPPDSPGYFDGHVWPmYLKYRQEmQDITWEVVYLDGTKSEEDLFLQVYEDLIQ 187
                                     8        18        28        38        48        58    |  |68     |  78  |      -   |    98       108       118       128       138       148 |     158       168       178         
                                                                                           63-MSE     74-MSE 81         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)

(no "SCOP Domain" information available for 2QT0)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) 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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NRK1_HUMAN | Q9NWW6: 2p0e 2qg6 2ql6 2qsy 2qsz 2qt1

(-) Related Entries Specified in the PDB File

2qsy HUMAN NICOTINAMIDE RIBOSIDE KINASE 1 IN COMPLEX WITH ADP
2qsz HUMAN NICOTINAMIDE RIBOSIDE KINASE 1 IN COMPLEX WITH NICOTINAMIDE MONONUCLEOTIDE
2qt1 HUMAN NICOTINAMIDE RIBOSIDE KINASE 1 IN COMPLEX WITH NICOTINAMIDE RIBOSIDE