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(-) Description

Title :  NH3-DEPENDENT NAD SYNTHETASE FROM CAMPYLOBACTER JEJUNI SUBSP. JEJUNI NCTC 11168 IN COMPLEX WITH THE NITRATE ION
 
Authors :  E. V. Filippova, Z. Wawrzak, O. Onopriyenko, T. Skarina, A. Edwards, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  07 Oct 10  (Deposition) - 27 Oct 10  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.74
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Nad+ Synthetase, Campylobacter Jejuni, Nade, Csgid, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. V. Filippova, Z. Wawrzak, O. Onopriyenko, T. Skarina, A. Edwards, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Nh3-Dependent Nad Synthetase From Campylobacter Jejuni Subsp. Jejuni Nctc 11168 In Complex With The Nitrate Ion
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 Plasmid: P15TV LIC
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CJ0810, NADE
    Organism Scientific: CAMPYLOBACTER JEJUNI
    Organism Taxid: 197

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2NO34Ligand/IonNITRATE ION
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2NO34Ligand/IonNITRATE ION
Biological Unit 2 (2, 54)
No.NameCountTypeFull Name
1MSE42Mod. Amino AcidSELENOMETHIONINE
2NO312Ligand/IonNITRATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:30 , SER A:31 , MSE A:56 , PRO A:57 , ARG A:112 , HOH A:249BINDING SITE FOR RESIDUE NO3 A 247
2AC2SOFTWARELEU B:30 , SER B:31 , LEU B:55 , MSE B:56 , PRO B:57 , ARG B:112 , HOH B:252BINDING SITE FOR RESIDUE NO3 B 247
3AC3SOFTWAREARG A:71 , ASN A:174 , ALA B:74 , ASP B:75BINDING SITE FOR RESIDUE NO3 B 248
4AC4SOFTWAREALA A:74 , ARG B:71 , HIS B:172 , ASN B:174BINDING SITE FOR RESIDUE NO3 B 249

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P52)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P52)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P52)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P52)

(-) Exons   (0, 0)

(no "Exon" information available for 3P52)

(-) 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:229
 aligned with NADE_CAMJE | Q9PPB0 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:246
                             1                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239      
           NADE_CAMJE     - -MDWQKITEKMCDFIQEKVKNSQSQGVVLGLSGGIDSALVATLCKRALKENVFALLMPTQISNKANLEDALRLCADLNLEYKIIEIQSILDAFIKQSENTTLVSLGNFAARIRMSLLYDYSALKNSLVIGTSNKSELLLGYGTIYGDLACAFNPIGSLYKSEIYALAKYLNLHENFIKKAPSADLWENQSDEADLGFSYTKIDEGLKALETNDEKLLRTLDPSLIAMLKNRMQKNAFKGKMPEILE 245
               SCOP domains d3p52a_ A: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhh.eeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eee....hhhhhhhh...........ee.....hhhhhhhhhhhh..hhhhhhh-----------------...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p52 A   0 AmDWQKITEKmCDFIQEKVKNSQSQGVVLGLSGGIDSALVATLCKRALKENVFALLmPTQISNKANLEDALRLCADLNLEYKIIEIQSILDAFIKQSENTTLVSLGNFAARIRmSLLYDYSALKNSLVIGTSNKSELLLGYGTIYGDLACAFNPIGSLYKSEIYALAKYLNLHENFIKK-----------------FSYTKIDEGLKALETNDEKLLRTLDPSLIAmLKNRmQKNAFKGKmPEILE 245
                             |       9|       19        29        39        49      | 59        69        79        89        99       109   |   119       129       139       149       159       169        |-         -      |199       209       219      |229 |     239|     
                             |       10-MSE                                        56-MSE                                                  113-MSE                                                          178               196                           226-MSE|      240-MSE 
                             1-MSE                                                                                                                                                                                                                               231-MSE          


Chain B from PDB  Type:PROTEIN  Length:229
 aligned with NADE_CAMJE | Q9PPB0 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
           NADE_CAMJE     1 MDWQKITEKMCDFIQEKVKNSQSQGVVLGLSGGIDSALVATLCKRALKENVFALLMPTQISNKANLEDALRLCADLNLEYKIIEIQSILDAFIKQSENTTLVSLGNFAARIRMSLLYDYSALKNSLVIGTSNKSELLLGYGTIYGDLACAFNPIGSLYKSEIYALAKYLNLHENFIKKAPSADLWENQSDEADLGFSYTKIDEGLKALETNDEKLLRTLDPSLIAMLKNRMQKNAFKGKMPEILE 245
               SCOP domains d3p52b_ B: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----NAD_synthase-3p52B01 B:6-241                                                                                                                                                                                                                ---- Pfam domains (1)
           Pfam domains (2) -----NAD_synthase-3p52B02 B:6-241                                                                                                                                                                                                                ---- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhh.eeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eee....hhhhhhhh...........ee.....hhhhhhhhhhhh..hhhhhhh----------------....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p52 B   1 mDWQKITEKmCDFIQEKVKNSQSQGVVLGLSGGIDSALVATLCKRALKENVFALLmPTQISNKANLEDALRLCADLNLEYKIIEIQSILDAFIKQSENTTLVSLGNFAARIRmSLLYDYSALKNSLVIGTSNKSELLLGYGTIYGDLACAFNPIGSLYKSEIYALAKYLNLHENFIKK----------------GFSYTKIDEGLKALETNDEKLLRTLDPSLIAmLKNRmQKNAFKGKmPEILE 245
                            |       10        20        30        40        50     |  60        70        80        90       100       110  |    120       130       140       150       160       170       | -         -    |  200       210       220     | 230|      240     
                            1-MSE   10-MSE                                        56-MSE                                                  113-MSE                                                          178              195                            226-MSE|      240-MSE 
                                                                                                                                                                                                                                                                231-MSE
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P52)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NADE_CAMJE | Q9PPB0)
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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