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Title :   CRYSTAL STRUCTURE OF AN NAD KINASE FROM ARCHAEOGLOBUS FULGIDUS IN COMPLEX WITH ATP

Authors :   J. Liu, Y. Lou, H. Yokota, P. D. Adams, R. Kim, S. H. Kim, Berkeley Structural Genomics Center (Bsgc)

Date :   02 Mar 05 (Deposition) - 19 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Nad Kinase, Atp-Binding, Structural Genomics, Nad, Nadp, Atp, Psi, Protein Structure Initiative, Berkeley Structural Genomics Center, Bsgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Liu, Y. Lou, H. Yokota, P. D. Adams, R. Kim, S. H. Kim
Crystal Structures Of An Nad Kinase From Archaeoglobus Fulgidus In Complex With Atp, Nad, Or Nadp
J. Mol. Biol. V. 354 289 2005
PubMed-ID: 16242716 | Reference-DOI: 10.1016/J.JMB.2005.09.026
(for further references see the PDB file header)

Molecule 1 - PROBABLE INORGANIC POLYPHOSPHATE/ATP-NAD KINASE
	Chains	:	A, B, C, D
	EC Number	:	2.7.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PB3.1114B
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PB3
	Gene	:	PPNK
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234
	Synonym	:	POLYP, /ATP NAD KINASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 12)

No.	Name	Count	Type	Full Name
1	ATP	4	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	POP	4	Ligand/Ion	PYROPHOSPHATE 2-

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ATP A:737 , POP A:3953	BINDING SITE FOR RESIDUE MG A 5001
02	AC2	SOFTWARE	ATP B:738 , POP B:3954	BINDING SITE FOR RESIDUE MG B 5002
03	AC3	SOFTWARE	ATP C:739 , POP C:3955	BINDING SITE FOR RESIDUE MG C 5003
04	AC4	SOFTWARE	ATP D:740 , POP D:3956	BINDING SITE FOR RESIDUE MG D 5004
05	AC5	SOFTWARE	GLY A:50 , ARG A:54 , ASN A:115 , GLU A:116 , GLY A:157 , TYR A:158 , SER A:161 , ASP A:209 , GLN A:211 , POP A:3953 , MG A:5001 , HOH A:5030 , HOH A:5079 , ALA D:125 , LYS D:126 , MET D:127 , ARG D:143 , ASP D:145 , ALA D:180 , PHE D:182 , HOH D:5036	BINDING SITE FOR RESIDUE ATP A 737
06	AC6	SOFTWARE	GLY B:50 , ARG B:54 , ASN B:115 , GLU B:116 , GLY B:157 , TYR B:158 , SER B:161 , ASP B:209 , GLN B:211 , POP B:3954 , MG B:5002 , HOH B:5029 , ALA C:125 , LYS C:126 , MET C:127 , ARG C:143 , ASP C:145 , ALA C:180 , PHE C:182 , HOH C:5083	BINDING SITE FOR RESIDUE ATP B 738
07	AC7	SOFTWARE	ALA B:125 , LYS B:126 , MET B:127 , ARG B:143 , ASP B:145 , ALA B:180 , PHE B:182 , HOH B:5035 , GLY C:50 , ARG C:54 , ASN C:115 , GLU C:116 , GLY C:157 , TYR C:158 , SER C:161 , ASP C:209 , GLN C:211 , POP C:3955 , MG C:5003 , HOH C:5067	BINDING SITE FOR RESIDUE ATP C 739
08	AC8	SOFTWARE	ALA A:125 , LYS A:126 , MET A:127 , ARG A:143 , ASP A:145 , ALA A:180 , PHE A:182 , HOH A:5035 , GLY D:50 , ARG D:54 , ASN D:115 , GLU D:116 , GLY D:157 , TYR D:158 , SER D:161 , ASP D:209 , GLN D:211 , POP D:3956 , MG D:5004 , HOH D:5028	BINDING SITE FOR RESIDUE ATP D 740
09	AC9	SOFTWARE	LYS A:8 , GLY A:48 , GLY A:50 , THR A:51 , ARG A:54 , GLY A:71 , ARG A:72 , ATP A:737 , MG A:5001 , HOH A:5079 , HOH A:5088	BINDING SITE FOR RESIDUE POP A 3953
10	BC1	SOFTWARE	LYS B:8 , GLY B:48 , GLY B:50 , THR B:51 , ARG B:54 , ARG B:72 , ATP B:738 , MG B:5002 , HOH B:5062	BINDING SITE FOR RESIDUE POP B 3954
11	BC2	SOFTWARE	LYS C:8 , GLY C:48 , ASP C:49 , GLY C:50 , THR C:51 , ARG C:54 , ARG C:72 , ATP C:739 , MG C:5003 , HOH C:5087	BINDING SITE FOR RESIDUE POP C 3955
12	BC3	SOFTWARE	LYS D:8 , GLY D:48 , GLY D:50 , THR D:51 , ARG D:54 , ARG D:72 , ATP D:740 , MG D:5004	BINDING SITE FOR RESIDUE POP D 3956

(no "SS Bond" information available for 1Z0S)

(no "Cis Peptide Bond" information available for 1Z0S)

(no "SAP(SNP)/Variant" information available for 1Z0S)

(no "PROSITE Motif" information available for 1Z0S)

(no "Exon" information available for 1Z0S)

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:249
 aligned with NADK_ARCFU | O30297 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           NADK_ARCFU     1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
               SCOP domains d1z0sa_ A: Inorganic polyphosphate/ATP-NAD kinase PpnK                                                                                                                                                                                                    SCOP domains
               CATH domains 1z0sA01 A:1-101,A:227-249 Probable inorganic polyphosphate/atp-NAD kinase; domain 1                  1z0sA02 A:102-226 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                  1z0sA01                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh..eeeee...hhhhhhh.eeeeeehhhhhhhhhh.......eeeee..............hhhhhhhhhhhh.eeee..eee..eeeeee..eeeeee......eeeeeee..eeeeeeee.eeeeee.hhhhhhhhhh...ee......eeeeee.........eee.....eeeeeeeeeeee...eeeeeeeeeeeee....eeee...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0s A   1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with NADK_ARCFU | O30297 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           NADK_ARCFU     1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
               SCOP domains d1z0sb_ B: Inorganic polyphosphate/ATP-NAD kinase PpnK                                                                                                                                                                                                    SCOP domains
               CATH domains 1z0sB01 B:1-101,B:227-249 Probable inorganic polyphosphate/atp-NAD kinase; domain 1                  1z0sB02 B:102-226 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                  1z0sB01                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh..eeeee...hhhhhhh.eeeeeehhhhhhhhhhh......eeeee..............hhhhhhhhhhhh.eeee..eee..eeeeee..eeeeee......eeeeeee..eeeeeeee.eeeeee.hhhhhhhhhh...ee......eeeeee.........eee.....eeeeeeeeeeee...eeeeeeeeeeeee....eeee...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0s B   1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain C from PDB  Type:PROTEIN  Length:249
 aligned with NADK_ARCFU | O30297 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           NADK_ARCFU     1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
               SCOP domains d1z0sc_ C: Inorganic polyphosphate/ATP-NAD kinase PpnK                                                                                                                                                                                                    SCOP domains
               CATH domains 1z0sC01 C:1-101,C:227-249 Probable inorganic polyphosphate/atp-NAD kinase; domain 1                  1z0sC02 C:102-226 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                  1z0sC01                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh..eeeee...hhhhhhh.eeeeeehhhhhhhhhh.......eeeee..............hhhhhhhhhhhh.eeee..eee..eeeeee..eeeeee......eeeeeee..eeeeeeee.eeeeee.hhhhhhhhhh...ee......eeeeee.........eee.....eeeeeeeeeeee...eeeeeeeeeeeee....eeee...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0s C   1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain D from PDB  Type:PROTEIN  Length:249
 aligned with NADK_ARCFU | O30297 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           NADK_ARCFU     1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
               SCOP domains d1z0sd_ D: Inorganic polyphosphate/ATP-NAD kinase PpnK                                                                                                                                                                                                    SCOP domains
               CATH domains 1z0sD01 D:1-101,D:227-249 Probable inorganic polyphosphate/atp-NAD kinase; domain 1                  1z0sD02 D:102-226 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                  1z0sD01                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh..eeeee...hhhhhhh.eeeeeehhhhhhhhhh.......eeeee..............hhhhhhhhhhhh.eeee..eee..eeeeee..eeeeee......eeeeeee..eeeeeeee.eeeeee.hhhhhhhhhh...ee......eeeeee.........eee.....eeeeeeeeeeee...eeeeeeeeeeeee....eeee...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0s D   1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Legend:		→ Mismatch	(orange background)
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	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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: NAD kinase/diacylglycerol kinase-like (15)

Superfamily: NAD kinase/diacylglycerol kinase-like (15)

Family: NAD kinase-like (8)

Protein domain: Inorganic polyphosphate/ATP-NAD kinase PpnK (8)

Archaeoglobus fulgidus [TaxId: 2234] (4)

1a	d1z0sa_	A:
1b	d1z0sb_	B:
1c	d1z0sc_	C:
1d	d1z0sd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Probable inorganic polyphosphate/atp-NAD kinase; domain 1 (8)

Archaeoglobus fulgidus. Organism_taxid: 2234. (3)

1a	1z0sA01	A:1-101,A:227-249
1b	1z0sB01	B:1-101,B:227-249
1c	1z0sC01	C:1-101,C:227-249
1d	1z0sD01	D:1-101,D:227-249

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Tumour Suppressor Smad4 (52)

Homologous Superfamily: Probable inorganic polyphosphate/atp-NAD kinase; domain 2 (9)

Archaeoglobus fulgidus. Organism_taxid: 2234. (3)

2a	1z0sA02	A:102-226
2b	1z0sB02	B:102-226
2c	1z0sC02	C:102-226
2d	1z0sD02	D:102-226

(no "Pfam Domain" information available for 1Z0S)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (NADK_ARCFU | O30297)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	1z0s
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	NADK_ARCFU \| O30297	:	1suw 1z0u 1z0z

(no "Related Entries Specified in the PDB File" available for 1Z0S)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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SCOP Domains (1, 4)

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