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(-) Description

Title :  NAD+ SYNTHETASE FROM BACILLUS ANTHRACIS WITH AMP + PPI AND MG2+
 
Authors :  H. M. Mcdonald, P. S. Pruett, C. Deivanayagam, I. I. Protasevich, W. M. C L. J. Delucas, W. J. Brouillette, C. G. Brouillette
Date :  17 May 07  (Deposition) - 31 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nad+ Synthetase, His-Tag, Bacillus Anthracis, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. M. Mcdonald, P. S. Pruett, C. Deivanayagam, I. I. Protasevich, W. M. Carson, L. J. Delucas, W. J. Brouillette, C. G. Brouillette
Structural Adaptation Of An Interacting Non-Native C-Terminal Helical Extension Revealed In The Crystal Structure Of Nad(+) Synthetase From Bacillus Anthracis.
Acta Crystallogr. , Sect. D V. 63 891 2007
PubMed-ID: 17642516  |  Reference-DOI: 10.1107/S0907444907029769

(-) 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: PET21B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NADE
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 1392

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3MG4Ligand/IonMAGNESIUM ION
4POP2Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR B:209 , AMP B:5000 , POP B:7000 , HOH B:7110 , HOH B:7111BINDING SITE FOR RESIDUE MG B 6240
02AC2SOFTWAREASP B:51 , GLU B:163 , AMP B:5000 , POP B:7000 , HOH B:7112BINDING SITE FOR RESIDUE MG B 6241
03AC3SOFTWAREASP A:51 , GLU A:163 , AMP A:4000 , POP A:6000 , HOH A:6362BINDING SITE FOR RESIDUE MG A 6242
04AC4SOFTWARETHR A:209 , AMP A:4000 , POP A:6000 , HOH A:6360 , HOH A:6361BINDING SITE FOR RESIDUE MG A 6243
05AC5SOFTWARELEU B:44 , GLY B:45 , ILE B:46 , SER B:47 , SER B:52 , ARG B:79 , LEU B:80 , GLN B:85 , ARG B:140 , THR B:158 , GLU B:163 , ASP B:174 , THR B:209 , ALA B:210 , MG B:6240 , MG B:6241 , POP B:7000 , HOH B:7003 , HOH B:7007 , HOH B:7008 , HOH B:7019 , HOH B:7110 , HOH B:7112BINDING SITE FOR RESIDUE AMP B 5000
06AC6SOFTWARELEU A:44 , GLY A:45 , ILE A:46 , SER A:47 , SER A:52 , ARG A:79 , LEU A:80 , GLN A:85 , ARG A:140 , THR A:158 , GLU A:163 , ASP A:174 , THR A:209 , ALA A:210 , POP A:6000 , MG A:6242 , MG A:6243 , HOH A:6247 , HOH A:6252 , HOH A:6258 , HOH A:6275 , HOH A:6285 , HOH A:6360BINDING SITE FOR RESIDUE AMP A 4000
07AC7SOFTWARESER B:47 , GLY B:49 , GLN B:50 , ASP B:51 , SER B:52 , GLU B:163 , LYS B:187 , PRO B:208 , THR B:209 , AMP B:5000 , MG B:6240 , MG B:6241 , HOH B:7007 , HOH B:7024 , HOH B:7110 , HOH B:7111 , HOH B:7112BINDING SITE FOR RESIDUE POP B 7000
08AC8SOFTWARESER A:47 , GLY A:49 , GLN A:50 , ASP A:51 , SER A:52 , GLU A:163 , LYS A:187 , PRO A:208 , THR A:209 , AMP A:4000 , MG A:6242 , MG A:6243 , HOH A:6278 , HOH A:6361BINDING SITE FOR RESIDUE POP A 6000
09AC9SOFTWARETYR B:82 , VAL B:84 , GLN B:85 , LYS B:86 , ASP B:211 , HOH B:7004 , HOH B:7029 , HOH B:7054BINDING SITE FOR RESIDUE GOL B 3308
10BC1SOFTWARETYR A:82 , VAL A:84 , GLN A:85 , LYS A:86 , ASP A:211 , HOH A:6296 , HOH A:6318BINDING SITE FOR RESIDUE GOL A 3309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PZA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PZA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PZA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PZA)

(-) Exons   (0, 0)

(no "Exon" information available for 2PZA)

(-) 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:279
 aligned with NADE_BACAN | Q81RP3 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:279
                                                                                                                                                                                                                                                                                                         272       
                                    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_BACAN     1 MTLQEQIMKALHVQPVIDPKAEIRKRVDFLKDYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVEEIRNEGGNATFIAVRLPYKVQKDEDDAQLALQFIQADQSVAFDIASTVDAFSNQYENLLDESLTDFNKGNVKARIRMVTQYAIGGQKGLLVIGTDHAAEAVTGFFTKFGDGGADLLPLTGLTKRQGRALLQELGADERLYLKMPTADLLDEKPGQADETELGITYDQLDDYLEGKTVPADVAEKIEKRYTVSEHKRQVPASMFDDWWK-------   -
               SCOP domains d2pzaa_ A: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2pzaA00 A:1-279 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...hhhhhhhhhhhhhhhhhhhhhhhhheee....hhhhhh....................hhhhhhhhhhhh..hhhhhhh.............hhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.......hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pza A   1 MTLQEQIMKALHVQPVIDPKAEIRKRVDFLKDYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVEEIRNEGGNATFIAVRLPYKVQKDEDDAQLALQFIQADQSVAFDIASTVDAFSNQYENLLDESLTDFNKGNVKARIRMVTQYAIGGQKGLLVIGTDHAAEAVTGFFTKFGDGGADLLPLTGLTKRQGRALLQELGADERLYLKMPTADLLDEKPGQADETELGITYDQLDDYLEGKTVPADVAEKIEKRYTVSEHKRQVPASMFDDWWKLAAALEH 279
                                    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:279
 aligned with NADE_BACAN | Q81RP3 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:279
                                                                                                                                                                                                                                                                                                         272       
                                    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_BACAN     1 MTLQEQIMKALHVQPVIDPKAEIRKRVDFLKDYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVEEIRNEGGNATFIAVRLPYKVQKDEDDAQLALQFIQADQSVAFDIASTVDAFSNQYENLLDESLTDFNKGNVKARIRMVTQYAIGGQKGLLVIGTDHAAEAVTGFFTKFGDGGADLLPLTGLTKRQGRALLQELGADERLYLKMPTADLLDEKPGQADETELGITYDQLDDYLEGKTVPADVAEKIEKRYTVSEHKRQVPASMFDDWWK-------   -
               SCOP domains d2pzab_ B: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2pzaB00 B:1-279 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) ---------------------NAD_synthase-2pzaB01 B:22-263                                                                                                                                                                                                                     ---------------- Pfam domains (1)
           Pfam domains (2) ---------------------NAD_synthase-2pzaB02 B:22-263                                                                                                                                                                                                                     ---------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhhhhh....................hhhhhhhhhhhh..hhhhhhh.............hhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.......hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pza B   1 MTLQEQIMKALHVQPVIDPKAEIRKRVDFLKDYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVEEIRNEGGNATFIAVRLPYKVQKDEDDAQLALQFIQADQSVAFDIASTVDAFSNQYENLLDESLTDFNKGNVKARIRMVTQYAIGGQKGLLVIGTDHAAEAVTGFFTKFGDGGADLLPLTGLTKRQGRALLQELGADERLYLKMPTADLLDEKPGQADETELGITYDQLDDYLEGKTVPADVAEKIEKRYTVSEHKRQVPASMFDDWWKLAAALEH 279
                                    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
   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  (1, 2)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NADE_BACAN | Q81RP3)
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.
    GO:0030436    asexual sporulation    The formation of spores derived from the products of an asexual cell division. Examples of this process are found in bacteria and fungi.

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  2pza
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 Related Entries

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

UniProtKB/Swiss-Prot
        NADE_BACAN | Q81RP3: 2pz8 2pzb

(-) Related Entries Specified in the PDB File

2pz8 THE SAME PROTEIN COMPLEXED WITH AMP-CPP.
2pzb