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(-) Description

Title :  CRYSTAL STRUCTURE OF LMNADK1
 
Authors :  G. Poncet-Montange, L. Assairi, S. Arold, S. Pochet, G. Labesse
Date :  16 Aug 06  (Deposition) - 07 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Crystal Structure Of Lmnadk1 Bound To A Nad Analog, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Poncet-Montange, L. Assairi, S. Arold, S. Pochet, G. Labesse
Nad Kinases Use Substrate-Assisted Catalysis For Specific Recognition Of Nad.
J. Biol. Chem. V. 282 33925 2007
PubMed-ID: 17686780  |  Reference-DOI: 10.1074/JBC.M701394200

(-) Compounds

Molecule 1 - PROBABLE INORGANIC POLYPHOSPHATE/ATP-NAD KINASE 1
    ChainsA
    EC Number2.7.1.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePPNK1
    MutationYES
    Organism ScientificLISTERIA MONOCYTOGENES
    Organism Taxid1639
    SynonymPOLYP, /ATP NAD KINASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:45 , GLY A:46 , NAD A:274BINDING SITE FOR RESIDUE PO4 A 273
2AC2SOFTWAREASN A:45 , PHE A:74 , TYR A:75 , ASN A:122 , GLU A:123 , PRO A:132 , ASP A:150 , THR A:161 , ALA A:162 , TYR A:163 , SER A:166 , ALA A:185 , ILE A:187 , TYR A:192 , HIS A:223 , PO4 A:273BINDING SITE FOR RESIDUE NAD A 274
3AC3SOFTWAREHIS A:173 , HIS A:205 , PRO A:252 , PHE A:253BINDING SITE FOR RESIDUE GOL A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I2F)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:113 -Lys A:114
2Gly A:130 -Gly A:131
3Asn A:213 -Asp A:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I2F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I2F)

(-) Exons   (0, 0)

(no "Exon" information available for 2I2F)

(-) Sequences/Alignments

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
(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:262
 aligned with NADK1_LISMO | Q8Y8D7 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:264
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
          NADK1_LISMO     1 MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKYGIGKKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIED 264
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhhhh....ee......eeeeeehhhhhhhhhhhh.......eeeeee..........hhhhhhhhhhhhhhh..eeeeeeeeeeeeee.--...eeeee..eeeeee....eeeeeee..eeeeeeee.eeeee.hhhhhhhhhhh..........eeeeeee..............eeee....eeeee.....eeeee..eeeee..eeeeeeeeeeeeeeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i2f A   1 MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGNGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKYG--KKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIED 264
                                    10        20        30        40        50        60        70        80        90       100       110  |    120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
                                                                                                                                       110  |                                                                                                                                                       
                                                                                                                                          113                                                                                                                                                       

   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 2I2F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2I2F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I2F)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (NADK1_LISMO | Q8Y8D7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    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: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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NADK1_LISMO | Q8Y8D72i1w 2i29 2i2a 2i2b 2i2c 2i2d 2q5f 3v7u 3v7w 3v7y 3v80 3v8m 3v8n 3v8p 3v8q 3v8r 4dy6 5dhp 5dhq 5dhr 5dhs 5dht 5dhu 5ejf 5ejg 5ejh 5eji

(-) Related Entries Specified in the PDB File

2i1w CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES
2i29 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES
2i2a CRYSTAL STRUCTURE OF LMNADK1 FROM LISTERIA MONOCYTOGENES
2i2b CRYSTAL STRUCTURE OF LMNADK1 FROM LISTERIA MONOCYTOGENES
2i2c CRYSTAL STRUCTURE OF LMNADK1
2i2d CRYSTAL STRUCTURE OF LMNADK1
2i2e CRYSTAL STRUCTURE OF LMNADK1