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(-) Description

Title :  1.9 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A NAD SYNTHETASE (NADE) FROM SALMONELLA TYPHIMURIUM LT2 IN COMPLEX WITH NAD(+)
 
Authors :  A. S. Halavaty, Z. Wawrzak, T. Skarina, O. Onopriyenko, S. N. Peterson, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  29 May 09  (Deposition) - 16 Jun 09  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nad Synthetase (Nade), Structural Genomics, Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Atp-Binding, Ligase, Nad, Nucleotide-Binding, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, Z. Wawrzak, T. Skarina, O. Onopriyenko, S. N. Peterson A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid
1. 9 Angstrom Resolution Crystal Structure Of A Nad Synthetase (Nade) From Salmonella Typhimurium Lt2 In Comple With Nad(+)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NH(3)-DEPENDENT NAD(+) SYNTHETASE
    Chains: A
    EC Number: 6.3.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-CODONPLUS(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NADE, STM1310
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 90371
    Strain: LT2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO48Ligand/IonSULFATE ION
Biological Unit 1 (3, 26)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO416Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:48 , GLY A:50 , ASP A:52 , SER A:53 , HOH A:385 , HOH A:483 , HOH A:547 , HOH A:552 , HOH A:610BINDING SITE FOR RESIDUE SO4 A 276
2AC2SOFTWARETYR A:85 , LYS A:138 , ARG A:142 , HOH A:523 , HOH A:638BINDING SITE FOR RESIDUE SO4 A 277
3AC3SOFTWAREGLY A:50 , GLN A:51 , LYS A:189 , HOH A:425 , HOH A:446 , HOH A:547BINDING SITE FOR RESIDUE SO4 A 278
4AC4SOFTWARETYR A:85 , ARG A:134 , LYS A:138 , HOH A:292 , HOH A:452 , HOH A:475BINDING SITE FOR RESIDUE SO4 A 279
5AC5SOFTWARENAD A:300 , HOH A:549 , HOH A:704BINDING SITE FOR RESIDUE SO4 A 280
6AC6SOFTWAREASP A:271 , PHE A:272 , HOH A:461 , HOH A:522BINDING SITE FOR RESIDUE SO4 A 281
7AC7SOFTWAREGLY A:86 , VAL A:87 , LYS A:112 , HOH A:497BINDING SITE FOR RESIDUE SO4 A 282
8AC8SOFTWARETHR A:2 , LEU A:3 , HOH A:519 , HOH A:686BINDING SITE FOR RESIDUE SO4 A 283
9AC9SOFTWARETYR A:33 , GLU A:70 , PHE A:132 , ASN A:136 , ARG A:140 , TYR A:147 , ALA A:150 , GLY A:151 , GLY A:155 , VAL A:156 , PHE A:170 , PHE A:171 , THR A:172 , LYS A:173 , ASP A:180 , ALA A:225 , TRP A:254 , HIS A:260 , LYS A:261 , SO4 A:280 , HOH A:337 , HOH A:438 , HOH A:508 , HOH A:565 , HOH A:586 , HOH A:628 , HOH A:655 , HOH A:665 , HOH A:672 , HOH A:684BINDING SITE FOR RESIDUE NAD A 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HMQ)

(-) 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:262
 aligned with NADE_SALTY | Q8ZPU5 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:275
                                    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     
           NADE_SALTY     1 MTLQQEIIQALGAKPHINPEEEIRRSVDFLKAYLKTYPFLKSLVLGISGGQDSTLAGKLSQMAIAELREETGDNALQFIAVRLPYGVQADEQDCQDAIAFIQPDRVLTVNIKGAVLASEQALREAGIELSDFVRGNEKARERMKAQYSIAGMTHGVVVGTDHAAEAITGFFTKYGDGGTDINPLHRLNKRQGKQLLAALGCPEHLYKKVPTADLEDDRPSLPDEAALGVTYDNIDDYLEGKTLDPAIAKTIEGWYVKTEHKRRLPITVFDDFWKR 275
               SCOP domains d3hmqa_ A: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.eee....hhhhhh....................hhhhhhhhhhhhh.hhhhh..-------------........hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hmq A   1 mTLQQEIIQALGAKPHINPEEEIRRSVDFLKAYLKTYPFLKSLVLGISGGQDSTLAGKLSQmAIAELREETGDNALQFIAVRLPYGVQADEQDCQDAIAFIQPDRVLTVNIKGAVLASEQALREAGIELSDFVRGNEKARERmKAQYSIAGmTHGVVVGTDHAAEAITGFFTKYGDGGTDINPLHRLNKRQGKQLLAALGCPEHLYKK-------------PDEAALGVTYDNIDDYLEGKTLDPAIAKTIEGWYVKTEHKRRLPITVFDDFWKR 275
                            |       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     
                            |                                                           62-MSE                                                                          143-MSE  152-MSE                                                 208           222                                                     
                            1-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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (NADE_SALTY | Q8ZPU5)
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.
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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