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(-) Description

Title :  CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE ATP, TWO MOLECULES DEAMIDO-NAD+ AND ONE MG2+ ION
 
Authors :  Y. Devedjiev, J. Symersky, R. Singh, M. Jedrzejas, C. Brouillette, W. Brouillette, D. Muccio, D. Chattopadhyay, L. Delucas
Date :  28 Jan 00  (Deposition) - 06 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lyase, Amidotransferase, Nh3 Dependent, Atp Pyrophosphatase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Devedjiev, J. Symersky, R. Singh, M. Jedrzejas, C. Brouillette, W. Brouillette, D. Muccio, D. Chattopadhyay, L. Delucas
Stabilization Of Active-Site Loops In Nh3-Dependent Nad+ Synthetase From Bacillus Subtilis.
Acta Crystallogr. , Sect. D V. 57 806 2001
PubMed-ID: 11375500  |  Reference-DOI: 10.1107/S0907444901003523
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NH(3)-DEPENDENT NAD(+) SYNTHETASE
    Chains: A, B
    EC Number: 6.3.5.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NADE
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: NAD(+) SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2DND2Ligand/IonNICOTINIC ACID ADENINE DINUCLEOTIDE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:208 , HOH A:2381 , HOH A:2382 , ATP A:5000BINDING SITE FOR RESIDUE MG A 5500
2AC2SOFTWAREPHE A:129 , ASN A:133 , ARG A:137 , PHE A:167 , PHE A:168 , THR A:169 , LYS A:170 , ASP A:173 , ALA A:209 , LEU A:211 , GLU A:223 , HIS A:257 , LYS A:258 , HOH A:2101 , HOH A:2158 , HOH A:2206 , HOH A:2213 , HOH A:2223 , HOH A:2238 , HOH A:2284 , ATP A:5000 , TYR B:32 , THR B:36 , TYR B:144 , LEU B:153 , ASP B:177 , HOH B:2071BINDING SITE FOR RESIDUE DND A 4000
3AC3SOFTWARETYR A:32 , THR A:36 , TYR A:144 , LEU A:153 , ASP A:177 , HOH A:2027 , PHE B:129 , ASN B:133 , ARG B:137 , PHE B:167 , PHE B:168 , THR B:169 , LYS B:170 , ASP B:173 , HIS B:257 , LYS B:258 , HOH B:2127 , HOH B:2228 , HOH B:2270 , HOH B:2304 , HOH B:2372 , HOH B:2377BINDING SITE FOR RESIDUE DND B 3000
4AC4SOFTWARELEU A:43 , GLY A:44 , ILE A:45 , SER A:46 , GLY A:48 , ASP A:50 , SER A:51 , ARG A:78 , LEU A:79 , GLN A:84 , ARG A:139 , THR A:157 , ASP A:173 , LYS A:186 , PRO A:207 , THR A:208 , HOH A:2012 , HOH A:2019 , HOH A:2023 , HOH A:2062 , HOH A:2080 , HOH A:2238 , HOH A:2284 , HOH A:2326 , HOH A:2381 , HOH A:2382 , DND A:4000 , MG A:5500BINDING SITE FOR RESIDUE ATP A 5000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EE1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EE1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EE1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EE1)

(-) Exons   (0, 0)

(no "Exon" information available for 1EE1)

(-) Sequences/Alignments

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:271
 aligned with NADE_BACSU | P08164 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:271
                                    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_BACSU     2 SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVESIREEGGDAQFIAVRLPHGTQQDEDDAQLALKFIKPDKSWKFDIKSTVSAFSDQYQQETGDQLTDFNKGNVKARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTKYGDGGADLLPLTGLTKRQGRTLLKELGAPERLYLKEPTADLLDEKPQQSDETELGISYDEIDDYLEGKEVSAKVSEALEKRYSMTEHKRQVPASMFDDWWK 272
               SCOP domains d1ee1a_ A: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ee1A00 A:1-271 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.........hhhh......................hhhhhhhhhhh...hhhhh...............hhhhh...hhhhhhhh......hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ee1 A   1 SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVESIREEGGDAQFIAVRLPHGTQQDEDDAQLALKFIKPDKSWKFDIKSTVSAFSDQYQQETGDQLTDFNKGNVKARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTKYGDGGADLLPLTGLTKRQGRTLLKELGAPERLYLKEPTADLLDEKPQQSDETELGISYDEIDDYLEGKEVSAKVSEALEKRYSMTEHKRQVPASMFDDWWK 271
                                    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       270 


Chain B from PDB  Type:PROTEIN  Length:246
 aligned with NADE_BACSU | P08164 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:271
                                    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_BACSU     2 SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVESIREEGGDAQFIAVRLPHGTQQDEDDAQLALKFIKPDKSWKFDIKSTVSAFSDQYQQETGDQLTDFNKGNVKARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTKYGDGGADLLPLTGLTKRQGRTLLKELGAPERLYLKEPTADLLDEKPQQSDETELGISYDEIDDYLEGKEVSAKVSEALEKRYSMTEHKRQVPASMFDDWWK 272
               SCOP domains d1ee1b_ B: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ee1B00 B:1-271 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh........hhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhh.....eeeeee....----hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.........hhhh......................hhhhhhhhhh....hhhh.---------------------..hhhhhhhh......hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ee1 B   1 SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVESIREEGGDAQFIAVRLPHG----EDDAQLALKFIKPDKSWKFDIKSTVSAFSDQYQQETGDQLTDFNKGNVKARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTKYGDGGADLLPLTGLTKRQGRTLLKELGAPERLYL---------------------ISYDEIDDYLEGKEVSAKVSEALEKRYSMTEHKRQVPASMFDDWWK 271
                                    10        20        30        40        50        60        70        80 |    | 90       100       110       120       130       140       150       160       170       180       190       200   |     -         -     | 230       240       250       260       270 
                                                                                                            82   87                                                                                                                  204                   226
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EE1)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NADE_BACSU | P08164)
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: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:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        NADE_BACSU | P08164: 1fyd 1ifx 1ih8 1kqp 1nsy 2nsy

(-) Related Entries Specified in the PDB File

1ifx ONTAINS THE SAME PROTEIN COMPEXED WITH TWO MOLECULES DEAMIDO-NAD
1nsy 1NSY CONTAINS THE SAME PROTEIN COMPLEXED WITH 2 MOL AMP, TWO PP - IONS, TWO MOLECULES ATP AND TWO MG2+ IONS