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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NAD KINASE
 
Authors :  H. Wang, W. Tempel, A. K. Wernimont, Y. Tong, X. Guan, Y. Shen, Y. Li, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, H. Park, Struc Genomics Consortium (Sgc)
Date :  28 Oct 10  (Deposition) - 10 Nov 10  (Release) - 10 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics Consortium, Snp, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wang, W. Tempel, A. K. Wernimont, Y. Tong, X. Guan, Y. Shen, Y. Li, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, H. Park
Crystal Structure Of Human Nad Kinase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NAD KINASE
    Chains: A, B, C, D
    EC Number: 2.7.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-CH
    Expression System Strain: BL21(DE3)-V2R-PRARE2
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 68-426
    Gene: NADK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POLY(P)/ATP NAD KINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 97)

Asymmetric/Biological Unit (2, 97)
No.NameCountTypeFull Name
1MSE35Mod. Amino AcidSELENOMETHIONINE
2UNX62Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 3PFN)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PFN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PFN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PFN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PFN)

(-) Exons   (0, 0)

(no "Exon" information available for 3PFN)

(-) 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:327
 aligned with NADK_HUMAN | O95544 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:356
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421      
           NADK_HUMAN    72 TTFGPKACVLQNPQTIMHIQDPASQRLTWNKSPKSVLVIKKMRDASLLQPFKELCTHLMEENMIVYVEKKVLEDPAIASDESFGAVKKKFCTFREDYDDISNQIDFIICLGGDGTLLYASSLFQGSVPPVMAFHLGSLGFLTPFSFENFQSQVTQVIEGNAAVVLRSRLKVRVVKELRGKKTAVHNGLGENGSQAAGLDMDVGKQAMQYQVLNEVVIDRGPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAAAAGASMIHPNVPAIMITPICPHSLSFRPIVVPAGVELKIMLSPEARNTAWVSFDGRKRQEIRHGDSISITTSCYPLPSICVRDPVSDWFESLAQCLHW 427
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eee......eeeee......eee.....eeeeee...hhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh..hhhhhhhheee............eeeee...hhhhhhhhhh......eeeee.........ee..hhhhhhhhhhhh...eeee..eeeeee.-----------------------------..eeeee..eeeee.........eeeee..eeeeee...eeeee.hhhhhhhhhhh...ee......eeeeee.........eee.....eeeee.......eeeee..eeeeee....eeeeee....eeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pfn A  72 TTFGPKACVLQNPQTImHIQDPASQRLTWNKSPKSVLVIKKmRDASLLQPFKELCTHLmEENmIVYVEKKVLEDPAIASDESFGAVKKKFCTFREDYDDISNQIDFIICLGGDGTLLYASSLFQGSVPPVmAFHLGSLGFLTPFSFENFQSQVTQVIEGNAAVVLRSRLKVRVVK-----------------------------QAmQYQVLNEVVIDRGPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAAAAGASmIHPNVPAImITPICPHSLSFRPIVVPAGVELKImLSPEARNTAWVSFDGRKRQEIRHGDSISITTSCYPLPSICVRDPVSDWFESLAQCLHH 427
                                    81      | 91       101       111 |     121       131  |    141       151       161       171       181       191       201|      211       221       231       241    |    -         -         -    | |281       291       301       311       321       331   |   341  |    351       361       371       381       391       401       411       421      
                                           88-MSE                  113-MSE          130-MSE                                                                 202-MSE                                     246                           276 |                                                      335-MSE  344-MSE                  369-MSE                                                      
                                                                                        134-MSE                                                                                                                                         278-MSE                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:327
 aligned with NADK_HUMAN | O95544 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:359
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418         
           NADK_HUMAN    69 CPVTTFGPKACVLQNPQTIMHIQDPASQRLTWNKSPKSVLVIKKMRDASLLQPFKELCTHLMEENMIVYVEKKVLEDPAIASDESFGAVKKKFCTFREDYDDISNQIDFIICLGGDGTLLYASSLFQGSVPPVMAFHLGSLGFLTPFSFENFQSQVTQVIEGNAAVVLRSRLKVRVVKELRGKKTAVHNGLGENGSQAAGLDMDVGKQAMQYQVLNEVVIDRGPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAAAAGASMIHPNVPAIMITPICPHSLSFRPIVVPAGVELKIMLSPEARNTAWVSFDGRKRQEIRHGDSISITTSCYPLPSICVRDPVSDWFESLAQCLHW 427
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eee......eeeee......eee.....eeeeee...hhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh...hhhhhhhheee............eeeee...hhhhhhhhhh......eeeee.........ee..hhhhhhhhhhhh...eeee..eeeeee.-----------------------------..eeeee..eeeeee..---...eeeee..eeeeee.eeeeeee.hhhhhhhhhhh...ee......eeeeeeee.......eee.....eeeee.......eeeee..eeeeee....eeeeee....eeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pfn B  69 CPVTTFGPKACVLQNPQTImHIQDPASQRLTWNKSPKSVLVIKKmRDASLLQPFKELCTHLmEENmIVYVEKKVLEDPAIASDESFGAVKKKFCTFREDYDDISNQIDFIICLGGDGTLLYASSLFQGSVPPVmAFHLGSLGFLTPFSFENFQSQVTQVIEGNAAVVLRSRLKVRVVK-----------------------------QAmQYQVLNEVVIDRGP---LSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAAAAGASmIHPNVPAImITPICPHSLSFRPIVVPAGVELKImLSPEARNTAWVSFDGRKRQEIRHGDSISITTSCYPLPSICVRDPVSDWFESLAQCLHH 427
                                    78        88        98       108    |  118       128 |   | 138       148       158       168       178       188       198   |   208       218       228       238       | -         -         -       278       288   |   298       308       318       328      |338     | 348       358       368|      378       388       398       408       418         
                                              88-MSE                  113-MSE          130-MSE                                                                 202-MSE                                     246                           276 |           292 296                                    335-MSE  344-MSE                  369-MSE                                                      
                                                                                           134-MSE                                                                                                                                         278-MSE                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:321
 aligned with NADK_HUMAN | O95544 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:356
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421      
           NADK_HUMAN    72 TTFGPKACVLQNPQTIMHIQDPASQRLTWNKSPKSVLVIKKMRDASLLQPFKELCTHLMEENMIVYVEKKVLEDPAIASDESFGAVKKKFCTFREDYDDISNQIDFIICLGGDGTLLYASSLFQGSVPPVMAFHLGSLGFLTPFSFENFQSQVTQVIEGNAAVVLRSRLKVRVVKELRGKKTAVHNGLGENGSQAAGLDMDVGKQAMQYQVLNEVVIDRGPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAAAAGASMIHPNVPAIMITPICPHSLSFRPIVVPAGVELKIMLSPEARNTAWVSFDGRKRQEIRHGDSISITTSCYPLPSICVRDPVSDWFESLAQCLHW 427
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eee.----....ee......eee.....eeeeee..--..hhhhhhhhhhhhhhh..eeeeehhhhhh...--...hhhhhhhheee............eeeee...hhhhhhhhhh......eeeee.........ee..hhhhhhhhhhhh...eeee..eeeeeee..-------------------------..eeeeeee..eeeeee..--....eeeee..eeeeee.eeeeeee.hhhhhhhhhhh...ee......eeeeeeee.......eee.....eeeee.......eeeee..eeeeee....eeeeee....eeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pfn C  72 TTFGPKACVL----TImHIQDPASQRLTWNKSPKSVLVIKKm--ASLLQPFKELCTHLmEENmIVYVEKKVLEDPAI--DESFGAVKKKFCTFREDYDDISNQIDFIICLGGDGTLLYASSLFQGSVPPVmAFHLGSLGFLTPFSFENFQSQVTQVIEGNAAVVLRSRLKVRVVKEL-------------------------GKQAmQYQVLNEVVIDRGP--YLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAAAAGASmIHPNVPAImITPICPHSLSFRPIVVPAGVELKImLSPEARNTAWVSFDGRKRQEIRHGDSISITTSCYPLPSICVRDPVSDWFESLAQCLHH 427
                                    81    | | 91       101       111 |  |  121       131  |    141      |151       161       171       181       191       201|      211       221       231       241      |  -         -         -  |   |281       291|  |   301       311       321       331   |   341  |    351       361       371       381       391       401       411       421      
                                    81   86 |                      113-MSE          130-MSE           148  |                                                202-MSE                                       248                       274   |           292  |                                     335-MSE  344-MSE                  369-MSE                                                      
                                           88-MSE                     116               134-MSE          151                                                                                                                            278-MSE          295                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:317
 aligned with NADK_HUMAN | O95544 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:357
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       
           NADK_HUMAN    69 CPVTTFGPKACVLQNPQTIMHIQDPASQRLTWNKSPKSVLVIKKMRDASLLQPFKELCTHLMEENMIVYVEKKVLEDPAIASDESFGAVKKKFCTFREDYDDISNQIDFIICLGGDGTLLYASSLFQGSVPPVMAFHLGSLGFLTPFSFENFQSQVTQVIEGNAAVVLRSRLKVRVVKELRGKKTAVHNGLGENGSQAAGLDMDVGKQAMQYQVLNEVVIDRGPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAAAAGASMIHPNVPAIMITPICPHSLSFRPIVVPAGVELKIMLSPEARNTAWVSFDGRKRQEIRHGDSISITTSCYPLPSICVRDPVSDWFESLAQCL 425
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------    ---- -----------NAD_kinase    -3pfnD01 D:102-410                                                                                                                                                                                                                                                                                     --------------- Pfam domains (1)
           Pfam domains (2) -------------    ---- -----------NAD_kinase    -3pfnD02 D:102-410                                                                                                                                                                                                                                                                                     --------------- Pfam domains (2)
           Pfam domains (3) -------------    ---- -----------NAD_kinase    -3pfnD03 D:102-410                                                                                                                                                                                                                                                                                     --------------- Pfam domains (3)
           Pfam domains (4) -------------    ---- -----------NAD_kinase    -3pfnD04 D:102-410                                                                                                                                                                                                                                                                                     --------------- Pfam domains (4)
         Sec.struct. author ....ee...eee.----.ee.-.......eee.....eeeee.----..hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh...hhhhhhhheee............eeeee...hhhhhhhhhh......eeeee.........ee..hhhhhhhhhhh--..eeee..eeeeee.-----------------------------..eeeee..eeeee.........eeeee..eeeeee.eeeeeee.hhhhhhhhhhh...ee......eeeeeeee.......eee.....eeeee.......eeeee..eeeeee....eeeeee....eeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pfn D  69 CPVTTFGPKACVL----TImH-QDPASQRLTWNKSPKSVLVIK----ASLLQPFKELCTHLmEENmIVYVEKKVLEDPAIASDESFGAVKKKFCTFREDYDDISNQIDFIICLGGDGTLLYASSLFQGSVPPVmAFHLGSLGFLTPFSFENFQSQVTQVIE--AAVVLRSRLKVRVVK-----------------------------QAmQYQVLNEVVIDRGPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAAAAGASmIHPNVPAImITPICPHSLSFRPIVVPAGVELKImLSPEARNTAWVSFDGRKRQEIRHGDSISITTSCYPLPSICVRDPVSDWFESLAQCL 425
                                    78  |    |88| |     98       108  |    118       128 |   | 138       148       158       168       178       188       198   |   208       218       228|  |   238       | -         -         -       278       288       298       308       318       328      |338     | 348       358       368|      378       388       398       408       418       
                                       81   86 || |                 111  116           130-MSE                                                                 202-MSE                    229  |           246                           276 |                                                      335-MSE  344-MSE                  369-MSE                                                    
                                              88-MSE                                       134-MSE                                                                                           232                                           278-MSE                                                                                                                                               
                                               89 |                                                                                                                                                                                                                                                                                                                                              
                                                 91
   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 3PFN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PFN)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: PFK (5)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (NADK_HUMAN | O95544)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003951    NAD+ kinase activity    Catalysis of the reaction: ATP + NAD(+) = ADP + 2 H(+) + NADP(+).
    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: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:0046034    ATP metabolic process    The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019674    NAD metabolic process    The chemical reactions and pathways involving nicotinamide adenine dinucleotide (NAD), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
    GO:0006741    NADP biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; biosynthesis may be of either the oxidized form, NADP, or the reduced form, NADPH.
    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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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