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(-) Description

Title :  E.COLI NAD SYNTHETASE, NAD
 
Authors :  R. Jauch, A. Humm, R. Huber, M. C. Wahl
Date :  23 Jan 05  (Deposition) - 15 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  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

Molecule 1 - NH(3)-DEPENDENT NAD(+) SYNTHETASE
    Chains: A
    EC Number: 6.3.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRSETHE
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: NAD SYNTHETASE, NITROGEN-REGULATORY PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:33 , GLU A:70 , THR A:71 , PHE A:132 , ASN A:136 , ARG A:140 , TYR A:147 , GLY A:155 , PHE A:170 , PHE A:171 , THR A:172 , LYS A:173 , ASP A:180 , VAL A:225 , ALA A:226 , TRP A:254 , HIS A:260 , LYS A:261 , HOH A:469 , HOH A:481 , HOH A:519 , HOH A:555 , HOH A:559 , HOH A:573 , HOH A:583 , HOH A:685BINDING SITE FOR RESIDUE NAD A 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WXH)

(-) 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:255
 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 d1wxha_ A: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1wxhA00 A:2-275 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------NAD_synthase-1wxhA01 A:22-265                                                                                                                                                                                                                       ---------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhhhhhhh....eeeeee.....---hhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..ee....hhhhhh....................hhhhhhhhhhhh..hhhhh.----------------......hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxh A   2 TLQQQIIKALGAKPQINAEEEIRRSVDFLKSYLQTYPFIKSLVLGISGGQDSTLAGKLCQMAINELRLETGNESLQFIAVRLPYGV---EQDCQDAIAFIQPDRVLTVNIKGAVLASEQALREAGIELSDFVRGNEKARERMKAQYSIAGMTSGVVVGTDHAAEAITGFFTKYGDGGTDINPLYRLNKRQGKQLLAALACPEHLYK----------------EVALGVTYDNIDDYLEGKNVPQQVARTIENWYLKTEHKRRPPITVFDDFWKK 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    
                                                                                                                87  91                                                                                                                 207              224
   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)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) 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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  1wxh
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 Related Entries

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

UniProtKB/Swiss-Prot
        NADE_ECOLI | P18843: 1wxe 1wxf 1wxg 1wxi

(-) Related Entries Specified in the PDB File

1wxe E.COLI NAD SYNTHETASE, AMP
1wxf E.COLI NAD SYNTHETASE
1wxg E.COLI NAD SYNTHETASE, DND
1wxi E.COLI NAD SYNTHETASE, AMP.PP