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(-) Description

Title :  CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES IN COMPLEX WITH 5'-AZIDO-5'-DEOXYADENOSINE
 
Authors :  M. Gelin, G. Poncet-Montange, L. Assairi, L. Morellato, V. Huteau, L. D O. Dussurget, S. Pochet, G. Labesse
Date :  22 Dec 11  (Deposition) - 14 Mar 12  (Release) - 27 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Ligand-Screening By Crystallography, Two-Domain Kinase, Inorganic Polyphosphate/Atp-Nad Kinase 1, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Gelin, G. Poncet-Montange, L. Assairi, L. Morellato, V. Huteau, L. Dugue, O. Dussurget, S. Pochet, G. Labesse
Screening And In Situ Synthesis Using Crystals Of A Nad Kinase Lead To A Potent Antistaphylococcal Compound.
Structure V. 20 1107 2012
PubMed-ID: 22608967  |  Reference-DOI: 10.1016/J.STR.2012.03.024

(-) Compounds

Molecule 1 - PROBABLE INORGANIC POLYPHOSPHATE/ATP-NAD KINASE 1
    Chains: A
    EC Number: 2.7.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PPNK1, LMO0968
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 1639
    Synonym: POLY(P)/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, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2GOL1Ligand/IonGLYCEROL
3ZAS2Ligand/Ion5'-AZIDO-5'-DEOXYADENOSINE
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2GOL4Ligand/IonGLYCEROL
3ZAS8Ligand/Ion5'-AZIDO-5'-DEOXYADENOSINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:45 , LEU A:72 , PHE A:74 , TYR A:75 , ASN A:122 , SER A:158 , THR A:161 , ALA A:162 , ILE A:187 , ASN A:189 , ZAS A:302 , HOH A:423 , HOH A:448 , HOH A:459 , HOH A:471BINDING SITE FOR RESIDUE ZAS A 301
2AC2SOFTWAREGLY A:46 , ASN A:122 , GLU A:123 , ASP A:150 , ALA A:162 , TYR A:163 , SER A:166 , ALA A:185 , ILE A:187 , ZAS A:301 , HOH A:423 , HOH A:431BINDING SITE FOR RESIDUE ZAS A 302
3AC3SOFTWAREVAL A:98 , TYR A:100 , HIS A:173 , ARG A:247 , PHE A:251 , PRO A:252 , PHE A:253 , HOH A:426 , HOH A:439 , HOH A:457BINDING SITE FOR RESIDUE CIT A 303
4AC4SOFTWARELYS A:8 , GLY A:44 , GLY A:46 , THR A:47 , GLY A:70 , HIS A:71 , HOH A:488BINDING SITE FOR RESIDUE GOL A 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V7W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V7W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V7W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V7W)

(-) Exons   (0, 0)

(no "Exon" information available for 3V7W)

(-) 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:260
 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 ..eeeee..hhhhhhhhhhhhhhhhh...........eeeeeehhhhhhhhhhhh.......eeeeee..........hhhhhhhhhhhhhhh..eeeeeeeeeeeee.----..eeeee..eeeeee....eeeeeee..eeeeeeee.eeeee.hhhhhhhhhhh..........eeeeeee..............eeee....eeeee.....eeeee..eeeee....eeeeeeeeeeeeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v7w A   1 MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKY----KEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIED 264
                                    10        20        30        40        50        60        70        80        90       100        |-   |   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
                                                                                                                                      109  114
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  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 3V7W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V7W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V7W)

(-) 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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  2.7.1.23
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 Related Entries

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

UniProtKB/Swiss-Prot
        NADK1_LISMO | Q8Y8D7: 2i1w 2i29 2i2a 2i2b 2i2c 2i2d 2i2f 2q5f 3v7u 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

2i2c 3v7v 3v7y 3v80 3v8m 3v8n 3v8p 3v8q 3v8r