3V80 - JenaLib

Title :   CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES IN COMPLEX WITH 5'-O-PROPARGYLAMINO-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 :   2.03

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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:49 , ASN A:122 , GLU A:123 , GLY A:149 , ASP A:150 , ALA A:162 , TYR A:163 , SER A:166 , ALA A:185 , ILE A:187 , HIS A:223 , AOC A:302 , HOH A:439	BINDING SITE FOR RESIDUE AOC A 301
2	AC2	SOFTWARE	ASP 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 , TYR A:192 , AOC A:301 , HOH A:439 , HOH A:440 , HOH A:462 , HOH A:477	BINDING SITE FOR RESIDUE AOC A 302
3	AC3	SOFTWARE	VAL A:98 , TYR A:100 , HIS A:173 , ARG A:247 , PHE A:251 , PRO A:252 , PHE A:253 , ARG A:256 , HOH A:423 , HOH A:434	BINDING SITE FOR RESIDUE CIT A 303
4	AC4	SOFTWARE	LYS A:8 , GLY A:44 , GLY A:46 , THR A:47 , HIS A:71 , HOH A:440 , HOH A:487	BINDING SITE FOR RESIDUE GOL A 304

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:258
 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......eeeee.hhhhhhhhhhhh.......eeeee...........hhhhhhhhhhhhh---.eeeeeeeeeeeee..---.eeeeee..eeeeee....eeeeeee..eeeeeeee.eeeee.hhhhhhhhhhh..........eeeeeee..............eeee....eeeee.....eeeee..eeeee....eeeeeeeeeeeeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v80 A   1 MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLA---YQKVSYPLLKTTVKYG---KEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIED 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    
                                                                                                                     91  95            110 114

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 (0, 0)

Pfam Domains (0, 0)

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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