Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH AMP-CPP AND MG2+ IONS.
 
Authors :  Y. Devedjiev, J. Symersky, R. Singh, M. Jedrzejas, C. Brouillette, W. Brouillette, D. Muccio, D. Chattopadhyay, L. Delucas
Date :  18 Apr 01  (Deposition) - 06 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Amidotransferase, Atp Pyrophosphatase, Active-Site Loops (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Devedjiev, J. Symersky, R. Singh, M. Jedrzejas, C. Brouillette, W. Brouillette, D. Muccio, D. Chattopadhyay, L. Delucas
Stabilization Of Active-Site Loops In Nh3-Dependent Nad+ Synthetase From Bacillus Subtilis.
Acta Crystallogr. , Sect. D V. 57 806 2001
PubMed-ID: 11375500  |  Reference-DOI: 10.1107/S0907444901003523
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NH(3)-DEPENDENT NAD(+) SYNTHETASE
    Chains: A, B
    EC Number: 6.3.5.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DH3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: OUTB
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: NAD(+) SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MG3Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:208 , HOH A:2385 , HOH A:2386 , APC A:3001BINDING SITE FOR RESIDUE MG A 4002
2AC2SOFTWAREGLU A:162 , HOH A:2060 , HOH A:2248 , HOH A:2387 , HOH A:2388 , APC A:3001BINDING SITE FOR RESIDUE MG A 4003
3AC3SOFTWAREASP B:1124 , HOH B:2280 , HOH B:2367 , HOH B:2480 , HOH B:2481 , HOH B:2482BINDING SITE FOR RESIDUE MG B 4004
4AC4SOFTWARELEU A:43 , GLY A:44 , ILE A:45 , SER A:46 , GLY A:48 , GLN A:49 , ASP A:50 , SER A:51 , ARG A:78 , LEU A:79 , GLN A:84 , ARG A:139 , THR A:157 , LYS A:186 , PRO A:207 , THR A:208 , ALA A:209 , HOH A:2036 , HOH A:2039 , HOH A:2040 , HOH A:2057 , HOH A:2117 , HOH A:2118 , HOH A:2125 , HOH A:2128 , HOH A:2385 , HOH A:2386 , HOH A:2388 , MG A:4002 , MG A:4003BINDING SITE FOR RESIDUE APC A 3001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IH8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IH8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IH8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IH8)

(-) Exons   (0, 0)

(no "Exon" information available for 1IH8)

(-) 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 d1ih8a_ A: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ih8A00 A:1-271 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhhhhh....................hhhhhhhhhhhh..hhhhhh..............hhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ih8 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:247
 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 d1ih8b_ B: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ih8B00 B:1001-1271 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhh....eeeeee....----hhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhheee....hhhhhhhh..................hhhhhhhhhhhh..hhhhhh--------------------..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ih8 B 1001 SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVESIREEGGDAQFIAVRLPHG----EDDAQLALKFIKPDKSWKFDIKSTVSAFSDQYQQETGDQLTDFNKGNVKARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTKYGDGGADLLPLTGLTKRQGRTLLKELGAPERLYL--------------------GISYDEIDDYLEGKEVSAKVSEALEKRYSMTEHKRQVPASMFDDWWK 1271
                                  1010      1020      1030      1040      1050      1060      1070      1080 |    1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200   |     -         -    | 1230      1240      1250      1260      1270 
                                                                                                          1082 1087                                                                                                                 1204                 1225
   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  (0, 0)

(no "Pfam Domain" information available for 1IH8)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    APC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ih8)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ih8
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NADE_BACSU | P08164
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.3.5.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  NADE_BACSU | P08164
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NADE_BACSU | P08164: 1ee1 1fyd 1ifx 1kqp 1nsy 2nsy

(-) Related Entries Specified in the PDB File

1ee1 1EE1 IS THE CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE ATP, TWO MOLECULES DEAMIDO-NAD+ AND ONE MG2+ ION
1fyd 1FYD IS THE CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE AMP, ONE PYROPHOSPHATE ION AND ONE MG2+ ION
1ifx 1IFX IS THE CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH TWO MOLECULES DEAMIDO-NAD
1nsy 1NSY IS THE CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS
2nsy 2NSY IS THE CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS IN COMPLEX WITH NAD- ADENYLATE