1WXI - JenaLib

Title :   E.COLI NAD SYNTHETASE, AMP.PP

Authors :   R. Jauch, A. Humm, R. Huber, M. C. Wahl

Date :   23 Jan 05 (Deposition) - 15 Feb 05 (Release) - 26 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Nade, Nad, E. Coli, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Jauch, A. Humm, R. Huber, M. C. Wahl
Structures Of Escherichia Coli Nad Synthetase With Substrates And Products Reveal Mechanistic Rearrangements
J. Biol. Chem. V. 280 15131 2005
PubMed-ID: 15699042 | Reference-DOI: 10.1074/JBC.M413195200

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:52 , GLU A:165 , AMP A:400 , DPO A:500 , HOH A:880	BINDING SITE FOR RESIDUE MG A 600
2	AC2	SOFTWARE	AMP A:400 , DPO A:500 , HOH A:729	BINDING SITE FOR RESIDUE MG A 700
3	AC3	SOFTWARE	TYR A:33 , ASN A:136 , ARG A:140 , TYR A:147 , GLY A:155 , PHE A:171 , THR A:172 , LYS A:173 , ASP A:180 , HIS A:260 , LYS A:261 , HOH A:775 , HOH A:799 , HOH A:879	BINDING SITE FOR RESIDUE AMP A 300
4	AC4	SOFTWARE	GLY A:46 , ILE A:47 , SER A:48 , SER A:53 , ARG A:82 , LEU A:83 , GLN A:88 , ARG A:142 , THR A:160 , GLU A:165 , ASP A:176 , DPO A:500 , MG A:600 , MG A:700 , HOH A:712 , HOH A:892	BINDING SITE FOR RESIDUE AMP A 400
5	AC5	SOFTWARE	SER A:48 , GLY A:50 , GLN A:51 , ASP A:52 , SER A:53 , GLU A:165 , LYS A:189 , AMP A:400 , MG A:600 , MG A:700 , HOH A:710 , HOH A:729 , HOH A:873 , HOH A:881	BINDING SITE FOR RESIDUE DPO A 500

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:261
 aligned with NADE_ECOLI | P18843 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
           NADE_ECOLI     2 TLQQQIIKALGAKPQINAEEEIRRSVDFLKSYLQTYPFIKSLVLGISGGQDSTLAGKLCQMAINELRLETGNESLQFIAVRLPYGVQADEQDCQDAIAFIQPDRVLTVNIKGAVLASEQALREAGIELSDFVRGNEKARERMKAQYSIAGMTSGVVVGTDHAAEAITGFFTKYGDGGTDINPLYRLNKRQGKQLLAALACPEHLYKKAPTADLEDDRPSLPDEVALGVTYDNIDDYLEGKNVPQQVARTIENWYLKTEHKRRPPITVFDDFWKK 275
               SCOP domains d1wxia_ A: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1wxiA00 A:2-275 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------NAD_synthase-1wxiA01 A:22-265                                                                                                                                                                                                                       ---------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.eee....hhhhhh....................hhhhhhhhhhhh..hhhhh...-------------hhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.......hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxi A   2 TLQQQIIKALGAKPQINAEEEIRRSVDFLKSYLQTYPFIKSLVLGISGGQDSTLAGKLCQMAINELRLETGNESLQFIAVRLPYGVQADEQDCQDAIAFIQPDRVLTVNIKGAVLASEQALREAGIELSDFVRGNEKARERMKAQYSIAGMTSGVVVGTDHAAEAITGFFTKYGDGGTDINPLYRLNKRQGKQLLAALACPEHLYKKA-------------DEVALGVTYDNIDDYLEGKNVPQQVARTIENWYLKTEHKRRPPITVFDDFWKK 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       | -         - |     231       241       251       261       271    
                                                                                                                                                                                                                                         209           223

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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (NADE_ECOLI | P18843)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003952	NAD+ synthase (glutamine-hydrolyzing) activity	Catalysis of the reaction: ATP + deamido-NAD+ + L-glutamine + H2O = AMP + diphosphate + NAD+ + L-glutamate.
	GO:0008795	NAD+ synthase activity	Catalysis of the reaction: ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	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.
biological process
	GO:0034628	'de novo' NAD biosynthetic process from aspartate	The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of aspartate from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
	GO:0009435	NAD biosynthetic process	The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
	GO:0034355	NAD salvage	Any process that generates nicotinamide adenine dinucleotide (NAD) from derivatives of it, without de novo synthesis; salvage is usually from the degradation products nicotinic acid (Na) and nicotinamide (Nam).
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
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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