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(-) Description

Title :  STRUCTURE OF NAD SYNTHETASE FROM VIBRIO CHOLERAE
 
Authors :  S. M. Anderson, Z. Wawrzak, O. Onopriyenko, S. N. Peterson, W. F. Anders A. Savchenko, Center For Structural Genomics Of Infectious Di (Csgid)
Date :  23 Dec 10  (Deposition) - 26 Jan 11  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Csgid, Center For Structural Genomics Of Infectious Diseases, Alpha Beta, 3-Layer(Aba) Sandwich, Rossmann Fold, Nad Synthetase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Anderson, Z. Wawrzak, O. Onopriyenko, S. N. Peterson, W. F. Anderson, A. Savchenko, Center For Structural Genomics Of Infectious Diseases (Csgid)
Structure Of Nad Synthetase From Vibrio Cholerae
To Be Published
PubMed: search

(-) 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 Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 11-285
    Gene: NADE, VCD_000045
    Mutation: YES
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 243277
    Strain: O1 BIOVAR ELTOR STR. N16961

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:58 , ASN A:65 , THR A:101BINDING SITE FOR RESIDUE CA A 277
2AC2SOFTWAREARG A:23 , PRO B:208 , GLN B:210BINDING SITE FOR RESIDUE CA A 278
3AC3SOFTWARESER A:45 , GLY A:47 , ASP A:49 , SER A:50 , HOH A:326BINDING SITE FOR RESIDUE CA A 279
4AC4SOFTWAREGLN B:58 , GLU B:62 , ASN B:65 , THR B:101BINDING SITE FOR RESIDUE CA B 277

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q4G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q4G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q4G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q4G)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q4G)

(-) 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:266
 aligned with NADE_VIBCH | Q9KMW1 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:279
                               1                                                                                                                                                                                                                                                                                   
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267         
           NADE_VIBCH     - ---MEHKIREEMRVLPSIDPQFEIERRVAFIKRKLTEARCKSLVLGISGGVDSTTCGRLAQLAVEELNQQHNTTEYQFIAVRLPYGEQKDEDEAQLALSFIRPTHSVSVNIKAGVDGLHAASHHALANTGLIPSDPAKVDFIKGNVKARARMVAQYEIAGYVGGLVLGTDHSAENITGFYTKFGDGACDLAPLFGLNKRQVRLLAKTLGAPEQLVYKTPTADLEELAPQKADEAALNLTYEQIDDFLEGKAVPAEVSQRLVAIYHATQHKRQPIPTIYD 276
               SCOP domains d3q4ga_ A: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhheee....hhhhhhhh..................hhhhhhhhhhhh..hhhhhh.......-------------..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q4g A  -2 SNAmEHKIREEmRVLPSIDPQFEIERRVAFIKRKLTEARYKSLVLGISGGVDSTTCGRLAQLAVEELNQQHNTTEYQFIAVRLPYGEQKDEDEAQLALSFIRPTHSVSVNIKAGVDGLHAASHHALANTGLIPSDPAKVDFIKGNVKARARmVAQYEIAGYVGGLVLGTDHSAENITGFYTKFGDGACDLAPLFGLNKRQVRLLAKTLGAPEQLVYKTPTADL-------------NLTYEQIDDFLEGKAVPAEVSQRLVAIYHATQHKRQPIPTIYD 276
                               |     7 |      17        27        37        47        57        67        77        87        97       107       117       127       137       147 |     157       167       177       187       197       207       217  |      -      |237       247       257       267         
                               |       9-MSE                                                                                                                                     149-MSE                                                                220           234                                          
                               1-MSE                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:257
 aligned with NADE_VIBCH | Q9KMW1 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:279
                               1                                                                                                                                                                                                                                                                                   
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267         
           NADE_VIBCH     - ---MEHKIREEMRVLPSIDPQFEIERRVAFIKRKLTEARCKSLVLGISGGVDSTTCGRLAQLAVEELNQQHNTTEYQFIAVRLPYGEQKDEDEAQLALSFIRPTHSVSVNIKAGVDGLHAASHHALANTGLIPSDPAKVDFIKGNVKARARMVAQYEIAGYVGGLVLGTDHSAENITGFYTKFGDGACDLAPLFGLNKRQVRLLAKTLGAPEQLVYKTPTADLEELAPQKADEAALNLTYEQIDDFLEGKAVPAEVSQRLVAIYHATQHKRQPIPTIYD 276
               SCOP domains d3q4gb_ B: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhh......---hhhhhhhhhhhhhhhhhhhhhhhhhheee....hhhhhhhh..................hhhhhhhhhhhhh.hhhhhh.-------------------..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q4g B  -2 SNAmEHKIREEmRVLPSIDPQFEIERRVAFIKRKLTEARYKSLVLGISGGVDSTTCGRLAQLAVEELNQQHNTTEYQFIAVRLPYGEQKDEDEAQLALSFIRPTHSVSVNIKAGVDGLHAASHHALANTGLIPS---KVDFIKGNVKARARmVAQYEIAGYVGGLVLGTDHSAENITGFYTKFGDGACDLAPLFGLNKRQVRLLAKTLGAPEQLVYK-------------------NLTYEQIDDFLEGKAVPAEVSQRLVAIYHATQHKRQPIPTIYD 276
                               |     7 |      17        27        37        47        57        67        77        87        97       107       117       127   |   137       147 |     157       167       177       187       197       207      |  -         -      |237       247       257       267         
                               1-MSE   9-MSE                                                                                                                   131 135           149-MSE                                                          214                 234
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "CATH Domain" information available for 3Q4G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3Q4G)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NADE_VIBCH | Q9KMW1)
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:0006734    NADH metabolic process    The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
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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