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(-) Description

Title :  CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS IN COMPLEX WITH NAD-ADENYLATE
 
Authors :  M. Rizzi, M. Bolognesi, A. Coda
Date :  14 Jul 98  (Deposition) - 13 Jan 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Amidotransferase, Nh3 Dependent, Atp Pyrophosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Rizzi, M. Bolognesi, A. Coda
A Novel Deamido-Nad+-Binding Site Revealed By The Trapped Nad-Adenylate Intermediate In The Nad+ Synthetase Structure
Structure V. 6 1129 1998
PubMed-ID: 9753692  |  Reference-DOI: 10.1016/S0969-2126(98)00114-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (NAD SYNTHETASE)
    Chains: A, B
    EC Number: 6.3.5.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3MG4Ligand/IonMAGNESIUM ION
4NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
5POP2Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:50 , GLU A:162 , AMP A:300 , HOH A:675 , POP A:863BINDING SITE FOR RESIDUE MG A 304
02AC2SOFTWARETHR A:208 , AMP A:300 , HOH A:676 , HOH A:677 , POP A:863BINDING SITE FOR RESIDUE MG A 305
03AC3SOFTWARETHR B:208 , AMP B:302 , HOH B:679 , HOH B:680 , POP B:862BINDING SITE FOR RESIDUE MG B 306
04AC4SOFTWAREASP B:50 , GLU B:162 , AMP B:302 , HOH B:678 , POP B:862BINDING SITE FOR RESIDUE MG B 307
05AC5SOFTWARELEU A:43 , GLY A:44 , ILE A:45 , SER A:46 , SER A:51 , ARG A:78 , LEU A:79 , GLN A:84 , ARG A:139 , THR A:157 , GLU A:162 , ASP A:173 , THR A:208 , ALA A:209 , NAD A:301 , MG A:304 , MG A:305 , HOH A:331 , HOH A:350 , HOH A:382 , HOH A:569 , HOH A:675 , HOH A:677 , POP A:863BINDING SITE FOR RESIDUE AMP A 300
06AC6SOFTWAREPHE 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 , AMP A:300 , HOH A:349 , HOH A:389 , HOH A:433 , HOH A:448 , HOH A:540 , HOH A:569 , HOH A:595 , HOH A:835 , TYR B:32 , THR B:36 , TYR B:144 , LEU B:153 , ASP B:177 , HOH B:347 , HOH B:468BINDING SITE FOR RESIDUE NAD A 301
07AC7SOFTWARELEU B:43 , GLY B:44 , ILE B:45 , SER B:46 , SER B:51 , ARG B:78 , LEU B:79 , GLN B:84 , ARG B:139 , THR B:157 , GLU B:162 , ASP B:173 , THR B:208 , ALA B:209 , NAD B:303 , MG B:306 , MG B:307 , HOH B:339 , HOH B:403 , HOH B:486 , HOH B:544 , HOH B:586 , HOH B:678 , HOH B:680 , POP B:862BINDING SITE FOR RESIDUE AMP B 302
08AC8SOFTWARETYR A:32 , THR A:36 , TYR A:144 , LEU A:153 , ASP A:177 , HOH A:424 , HOH A:585 , ASN B:133 , ARG B:137 , PHE B:167 , PHE B:168 , THR B:169 , LYS B:170 , ASP B:173 , ALA B:209 , LEU B:211 , GLU B:223 , HIS B:257 , LYS B:258 , AMP B:302 , HOH B:418 , HOH B:486 , HOH B:499 , HOH B:520 , HOH B:530 , HOH B:579 , HOH B:586 , HOH B:648 , HOH B:811 , HOH B:850BINDING SITE FOR RESIDUE NAD B 303
09AC9SOFTWARESER B:46 , GLY B:48 , GLN B:49 , ASP B:50 , SER B:51 , GLU B:162 , LYS B:186 , PRO B:207 , THR B:208 , AMP B:302 , MG B:306 , MG B:307 , HOH B:359 , HOH B:486 , HOH B:678 , HOH B:679 , HOH B:680BINDING SITE FOR RESIDUE POP B 862
10BC1SOFTWARESER A:46 , GLY A:48 , GLN A:49 , ASP A:50 , SER A:51 , GLU A:162 , LYS A:186 , PRO A:207 , THR A:208 , AMP A:300 , MG A:304 , MG A:305 , HOH A:311 , HOH A:349 , HOH A:675 , HOH A:676 , HOH A:677BINDING SITE FOR RESIDUE POP A 863
11BC2SOFTWAREASP A:158 , ALA A:163 , PHE A:168 , LYS A:258 , ARG A:259 , HOH A:800 , HOH A:801 , PRO B:262BINDING SITE FOR RESIDUE GOL A 308
12BC3SOFTWAREPRO A:262 , GLY B:174 , LYS B:258 , HOH B:332 , HOH B:463 , HOH B:607 , HOH B:799BINDING SITE FOR RESIDUE GOL B 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NSY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NSY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NSY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NSY)

(-) Exons   (0, 0)

(no "Exon" information available for 2NSY)

(-) 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 d2nsya_ A: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2nsyA00 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
                 2nsy 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: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 d2nsyb_ B: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2nsyB00 B:1-271 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                           CATH domains
           Pfam domains (1) --------------------NAD_synthase-2nsyB01 B:21-262                                                                                                                                                                                                                     --------- Pfam domains (1)
           Pfam domains (2) --------------------NAD_synthase-2nsyB02 B:21-262                                                                                                                                                                                                                     --------- Pfam domains (2)
         Sec.struct. author .hhhhhhhh........hhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhh.....eeeeee........hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.........hhhh......................hhhhhhhhhh....hhhh................hhhhh...hhhhhhhh......hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nsy B   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
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)

(-) 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: 1ee1 1fyd 1ifx 1ih8 1kqp 1nsy

(-) Related Entries Specified in the PDB File

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