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(-) Description

Title :  CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM HELICOBACTER PYLORI
 
Authors :  G. B. Kang, Y. S. Kim, Y. J. Im, S. H. Rho, J. H. Lee, S. H. Eom
Date :  05 Oct 04  (Deposition) - 05 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nh3-Dependent Nad+ Synthetase, Helicobacter Pylori, Amidotransferase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. B. Kang, Y. S. Kim, Y. J. Im, S. H. Rho, J. H. Lee, S. H. Eom
Crystal Structure Of Nh3-Dependent Nad+ Synthetase From Helicobacter Pylori
Proteins V. 58 985 2005
PubMed-ID: 15645437  |  Reference-DOI: 10.1002/PROT.20377
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NH(3)-DEPENDENT NAD(+) SYNTHETASE
    Chains: A, B
    EC Number: 6.3.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2DND2Ligand/IonNICOTINIC ACID ADENINE DINUCLEOTIDE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:183 , ATP B:304BINDING SITE FOR RESIDUE MG B 308
2AC2SOFTWARESER A:183 , ATP A:303 , HOH A:334 , HOH A:381BINDING SITE FOR RESIDUE MG A 309
3AC3SOFTWARETHR A:104 , ASN A:108 , ARG A:112 , TYR A:142 , GLY A:143 , THR A:144 , LEU A:145 , ASP A:148 , ALA A:184 , LEU A:186 , GLN A:190 , PHE A:246 , LYS A:247 , ATP A:303 , HOH A:318 , HOH A:320 , HOH A:329 , HOH A:346 , HOH A:347 , HOH A:362 , HOH A:371 , HOH A:383 , HOH A:390 , HOH A:392 , HOH A:400 , ARG B:23 , PHE B:25 , TYR B:119 , SER B:122 , LEU B:123 , LEU B:128 , ALA B:152 , HOH B:357BINDING SITE FOR RESIDUE DND A 301
4AC4SOFTWAREARG A:23 , PHE A:25 , TYR A:119 , SER A:122 , LEU A:123 , LEU A:128 , ALA A:152 , HOH A:312 , HOH A:405 , THR B:104 , ASN B:108 , ARG B:112 , TYR B:142 , GLY B:143 , THR B:144 , LEU B:145 , ASP B:148 , ALA B:184 , LEU B:186 , GLN B:190 , ASP B:195 , PHE B:246 , LYS B:247 , ATP B:304 , HOH B:318 , HOH B:319 , HOH B:343 , HOH B:369 , HOH B:373 , HOH B:381 , HOH B:383 , HOH B:395 , HOH B:420 , HOH B:429BINDING SITE FOR RESIDUE DND B 302
5AC5SOFTWAREGLY A:31 , LEU A:32 , SER A:33 , GLY A:35 , LEU A:36 , ASP A:37 , SER A:38 , LEU A:56 , MET A:58 , ARG A:114 , THR A:132 , GLU A:137 , LYS A:161 , PRO A:182 , SER A:183 , DND A:301 , MG A:309 , HOH A:324 , HOH A:338 , HOH A:376 , HOH A:383 , HOH A:413 , HOH A:423BINDING SITE FOR RESIDUE ATP A 303
6AC6SOFTWAREGLY B:31 , LEU B:32 , SER B:33 , GLY B:35 , LEU B:36 , ASP B:37 , SER B:38 , LEU B:56 , MET B:58 , ARG B:114 , THR B:132 , GLU B:137 , LYS B:161 , PRO B:182 , SER B:183 , DND B:302 , MG B:308 , HOH B:316 , HOH B:343 , HOH B:349 , HOH B:370 , HOH B:407BINDING SITE FOR RESIDUE ATP B 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XNG)

(-) 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:255
 aligned with NADE_HELPY | O25096 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:255
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252     
           NADE_HELPY     3 KDYQKLIVYLCDFLEKEVQKRGFKKVVYGLSGGLDSAVVGVLCQKVFKENAHALLMPSSVSMPENKTDALNLCEKFSIPYTEYSIAPYDAIFSSHFKDASLTRKGNFCARLRMAFLYDYSLKSDSLVIGTSNKSERMLGYGTLFGDLACAINPIGELFKTEVYELARRLNIPKKILNKPPSADLFVGQSDEKDLGYPYSVIDPLLKDIEALFQTKPIDTETLAQLGYDEILVKNITSRIQKNAFKLELPAIAKRF 257
               SCOP domains d1xnga1 A:3-257 NH3-dependent NAD+-synthetase                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhhhhhhh...........ee.....hhhhhhhhhhhh..hhhhhh...........hhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhh..hhhhhhhhhhhhhhhhhhhh..ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xng A   3 KDYQKLIVYLCDFLEKEVQKRGFKKVVYGLSGGLDSAVVGVLCQKVFKENAHALLMPSSVSMPENKTDALNLCEKFSIPYTEYSIAPYDAIFSSHFKDASLTRKGNFCARLRMAFLYDYSLKSDSLVIGTSNKSERMLGYGTLFGDLACAINPIGELFKTEVYELARRLNIPKKILNKPPSADLFVGQSDEKDLGYPYSVIDPLLKDIEALFQTKPIDTETLAQLGYDEILVKNITSRIQKNAFKLELPAIAKRF 257
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252     


Chain B from PDB  Type:PROTEIN  Length:262
 aligned with NADE_HELPY | O25096 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:262
                                                                                                                                                                                                                                                                                           260    
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       | -  
           NADE_HELPY     3 KDYQKLIVYLCDFLEKEVQKRGFKKVVYGLSGGLDSAVVGVLCQKVFKENAHALLMPSSVSMPENKTDALNLCEKFSIPYTEYSIAPYDAIFSSHFKDASLTRKGNFCARLRMAFLYDYSLKSDSLVIGTSNKSERMLGYGTLFGDLACAINPIGELFKTEVYELARRLNIPKKILNKPPSADLFVGQSDEKDLGYPYSVIDPLLKDIEALFQTKPIDTETLAQLGYDEILVKNITSRIQKNAFKLELPAIAKRFNPE----   -
               SCOP domains d1xngb_ B: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----NAD_synthase-1xngB01 B:8-251                                                                                                                                                                                                                        ------------- Pfam domains (1)
           Pfam domains (2) -----NAD_synthase-1xngB02 B:8-251                                                                                                                                                                                                                        ------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhh...eee..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhhhhhhh...........ee.....hhhhhhhhhhhh..hhhhhh...........hhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..ee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xng B   3 KDYQKLIVYLCDFLEKEVQKRGFKKVVYGLSGGLDSAVVGVLCQKVFKENAHALLMPSSVSMPENKTDALNLCEKFSIPYTEYSIAPYDAIFSSHFKDASLTRKGNFCARLRMAFLYDYSLKSDSLVIGTSNKSERMLGYGTLFGDLACAINPIGELFKTEVYELARRLNIPKKILNKPPSADLFVGQSDEKDLGYPYSVIDPLLKDIEALFQTKPIDTETLAQLGYDEILVKNITSRIQKNAFKLELPAIAKRFNPELEHH 264
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262
   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  (2, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XNG)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NADE_HELPY | O25096)
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.

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  1xng
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 Related Entries

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

UniProtKB/Swiss-Prot
        NADE_HELPY | O25096: 1xnh

(-) Related Entries Specified in the PDB File

1xnh THE SAME PROTEIN, NATIVE