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(-) Description

Title :  NAD+ SYNTHETASE FROM BACILLUS ANTHRACIS WITH AMP-CPP 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 :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Substrate Analog Complex, His-Tag, 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  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1APC2Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2GOL2Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:209 , APC A:3001 , HOH A:4133 , HOH A:4134BINDING SITE FOR RESIDUE MG A 4001
2AC2SOFTWARETHR B:209 , APC B:3002 , HOH B:4144 , HOH B:4145BINDING SITE FOR RESIDUE MG B 4002
3AC3SOFTWARELEU A:44 , GLY A:45 , ILE A:46 , SER A:47 , GLY A:49 , GLN A:50 , ASP A:51 , SER A:52 , ARG A:79 , LEU A:80 , GLN A:85 , ARG A:140 , THR A:158 , LYS A:187 , PRO A:208 , THR A:209 , MG A:4001 , HOH A:4028 , HOH A:4030 , HOH A:4034 , HOH A:4055 , HOH A:4087 , HOH A:4126 , HOH A:4133 , HOH A:4134BINDING SITE FOR RESIDUE APC A 3001
4AC4SOFTWARELEU B:44 , GLY B:45 , ILE B:46 , SER B:47 , GLY B:49 , GLN B:50 , ASP B:51 , SER B:52 , ARG B:79 , LEU B:80 , GLN B:85 , ARG B:140 , THR B:158 , ASP B:174 , LYS B:187 , PRO B:208 , THR B:209 , MG B:4002 , HOH B:4013 , HOH B:4014 , HOH B:4027 , HOH B:4037 , HOH B:4067 , HOH B:4110 , HOH B:4144 , HOH B:4145BINDING SITE FOR RESIDUE APC B 3002
5AC5SOFTWARETYR B:82 , VAL B:84 , GLN B:85 , LYS B:86 , ASP B:211 , HOH B:4024 , HOH B:4048 , HOH B:4061 , HOH B:4117BINDING SITE FOR RESIDUE GOL B 3308
6AC6SOFTWARETYR A:82 , VAL A:84 , GLN A:85 , LYS A:86 , ASP A:211 , HOH A:4022 , HOH A:4062 , HOH A:4093BINDING SITE FOR RESIDUE GOL A 3309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PZ8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PZ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PZ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PZ8)

(-) Exons   (0, 0)

(no "Exon" information available for 2PZ8)

(-) 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:280
 aligned with NADE_BACAN | Q81RP3 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:280
                                                                                                                                                                                                                                                                                                         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 d2pz8a_ A: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2pz8A00 A:1-280 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.............ee.....hhhhhhhhhhhh...hhhhhh.............hhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.......hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pz8 A   1 MTLQEQIMKALHVQPVIDPKAEIRKRVDFLKDYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVEEIRNEGGNATFIAVRLPYKVQKDEDDAQLALQFIQADQSVAFDIASTVDAFSNQYENLLDESLTDFNKGNVKARIRMVTQYAIGGQKGLLVIGTDHAAEAVTGFFTKFGDGGADLLPLTGLTKRQGRALLQELGADERLYLKMPTADLLDEKPGQADETELGITYDQLDDYLEGKTVPADVAEKIEKRYTVSEHKRQVPASMFDDWWKLAAALEHH 280
                                    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       280


Chain B from PDB  Type:PROTEIN  Length:280
 aligned with NADE_BACAN | Q81RP3 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:280
                                                                                                                                                                                                                                                                                                         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 d2pz8b_ B: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2pz8B00 B:1-280 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) ---------------------NAD_synthase-2pz8B01 B:22-263                                                                                                                                                                                                                     ----------------- Pfam domains (1)
           Pfam domains (2) ---------------------NAD_synthase-2pz8B02 B:22-263                                                                                                                                                                                                                     ----------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhheee....hhhhhh....................hhhhhhhhhhhh...hhhhhh.............hhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..ee...hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pz8 B   1 MTLQEQIMKALHVQPVIDPKAEIRKRVDFLKDYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVEEIRNEGGNATFIAVRLPYKVQKDEDDAQLALQFIQADQSVAFDIASTVDAFSNQYENLLDESLTDFNKGNVKARIRMVTQYAIGGQKGLLVIGTDHAAEAVTGFFTKFGDGGADLLPLTGLTKRQGRALLQELGADERLYLKMPTADLLDEKPGQADETELGITYDQLDDYLEGKTVPADVAEKIEKRYTVSEHKRQVPASMFDDWWKLAAALEHH 280
                                    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       280
   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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2pza 2pzb