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(-) Description

Title :  NAD+ SYNTHETASE FROM BACILLUS ANTHRACIS
 
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 :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:136 , ARG A:140 , HOH A:4888BINDING SITE FOR RESIDUE SO4 A 4770
02AC2SOFTWARELYS B:136 , ARG B:140 , HOH B:4862 , HOH B:4878BINDING SITE FOR RESIDUE SO4 B 4771
03AC3SOFTWARELYS C:136 , ARG C:140 , HOH C:4867BINDING SITE FOR RESIDUE SO4 C 4772
04AC4SOFTWARELYS D:136 , ARG D:140 , HOH D:4852 , HOH D:4855BINDING SITE FOR RESIDUE SO4 D 4773
05AC5SOFTWARESER A:47 , GLY A:49 , ASP A:51 , SER A:52 , THR A:158 , LYS A:171 , HOH A:4808 , HOH A:4840BINDING SITE FOR RESIDUE SO4 A 4774
06AC6SOFTWARESER B:47 , GLY B:49 , SER B:52 , THR B:158 , LYS B:171 , HOH B:4807 , HOH B:4902BINDING SITE FOR RESIDUE SO4 B 4775
07AC7SOFTWARESER C:47 , GLY C:49 , ASP C:51 , SER C:52 , THR C:158 , LYS C:171 , HOH C:4802BINDING SITE FOR RESIDUE SO4 C 4776
08AC8SOFTWARESER D:47 , GLY D:49 , ASP D:51 , SER D:52 , THR D:158 , LYS D:171 , HOH D:4819BINDING SITE FOR RESIDUE SO4 D 4777
09AC9SOFTWARETHR A:128 , ASP A:129 , PHE A:130 , HIS A:279 , HIS A:283 , HOH A:4787 , HOH A:4896 , HOH A:4901BINDING SITE FOR RESIDUE SO4 A 4778
10BC1SOFTWARETHR B:128 , ASP B:129 , PHE B:130 , HIS B:279 , HIS B:283 , HOH B:4790 , HOH B:4803 , HOH B:4897BINDING SITE FOR RESIDUE SO4 B 4779
11BC2SOFTWARETHR C:128 , ASP C:129 , PHE C:130 , HIS C:279 , HIS C:283 , HOH C:4817 , HOH C:4818BINDING SITE FOR RESIDUE SO4 C 4780
12BC3SOFTWARETHR D:128 , ASP D:129 , PHE D:130 , HIS D:279 , HOH D:4808 , HOH D:4887BINDING SITE FOR RESIDUE SO4 D 4781

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PZB)

(-) 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:250
 aligned with NADE_BACAN | Q81RP3 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:283
                                                                                                                                                                                                                                                                                                         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 d2pzba_ A: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2pzbA00 A:1-283 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhh....eeeeee.....---hhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhh..................hhhhhhhhhhhh..hhhhh.---------------------.hhhhhhhhhh....hhhhhhhhhhhhhhh---------hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzb A   1 MTLQEQIMKALHVQPVIDPKAEIRKRVDFLKDYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVEEIRNEGGNATFIAVRLPYKV---EDDAQLALQFIQADQSVAFDIASTVDAFSNQYENLLDESLTDFNKGNVKARIRMVTQYAIGGQKGLLVIGTDHAAEAVTGFFTKFGDGGADLLPLTGLTKRQGRALLQELGADERLYL---------------------ITYDQLDDYLEGKTVPADVAEKIEKRYTVS---------MFDDWWKLAAALEHHHHH 283
                                    10        20        30        40        50        60        70        80   |   |90       100       110       120       130       140       150       160       170       180       190       200    |    -         -      |230       240       250     |   -     | 270       280   
                                                                                                              84  88                                                                                                                  205                   227                          256       266                 


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with NADE_BACAN | Q81RP3 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:283
                                                                                                                                                                                                                                                                                                         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 d2pzbb_ B: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2pzbB00 B:1-283 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhh....eeeeee....----hhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhh..................hhhhhhhhhhhh..hhhhh.---------------------.hhhhhhhhhh....hhhhhhhhhhhhhh.---------hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzb B   1 MTLQEQIMKALHVQPVIDPKAEIRKRVDFLKDYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVEEIRNEGGNATFIAVRLPYK----EDDAQLALQFIQADQSVAFDIASTVDAFSNQYENLLDESLTDFNKGNVKARIRMVTQYAIGGQKGLLVIGTDHAAEAVTGFFTKFGDGGADLLPLTGLTKRQGRALLQELGADERLYL---------------------ITYDQLDDYLEGKTVPADVAEKIEKRYTVS---------MFDDWWKLAAALEHHHHH 283
                                    10        20        30        40        50        60        70        80  |    |90       100       110       120       130       140       150       160       170       180       190       200    |    -         -      |230       240       250     |   -     | 270       280   
                                                                                                             83   88                                                                                                                  205                   227                          256       266                 


Chain C from PDB  Type:PROTEIN  Length:247
 aligned with NADE_BACAN | Q81RP3 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:282
                                                                                                                                                                                                                                                                                                        272           
                                    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_BACAN     2 TLQEQIMKALHVQPVIDPKAEIRKRVDFLKDYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVEEIRNEGGNATFIAVRLPYKVQKDEDDAQLALQFIQADQSVAFDIASTVDAFSNQYENLLDESLTDFNKGNVKARIRMVTQYAIGGQKGLLVIGTDHAAEAVTGFFTKFGDGGADLLPLTGLTKRQGRALLQELGADERLYLKMPTADLLDEKPGQADETELGITYDQLDDYLEGKTVPADVAEKIEKRYTVSEHKRQVPASMFDDWWK-----------   -
               SCOP domains d2pzbc_ C: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2pzbC00 C:2-283 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhh....eeeeee....-----hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhh..................hhhhhhhhhhhh..hhhhhh---------------------.hhhhhhhhhh....hhhhhhhhhhhhhh.---------hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pzb C   2 TLQEQIMKALHVQPVIDPKAEIRKRVDFLKDYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVEEIRNEGGNATFIAVRLPYK-----DDAQLALQFIQADQSVAFDIASTVDAFSNQYENLLDESLTDFNKGNVKARIRMVTQYAIGGQKGLLVIGTDHAAEAVTGFFTKFGDGGADLLPLTGLTKRQGRALLQELGADERLYL---------------------ITYDQLDDYLEGKTVPADVAEKIEKRYTVS---------MFDDWWKLAAALEHHHHH 283
                                    11        21        31        41        51        61        71        81 |     |91       101       111       121       131       141       151       161       171       181       191       201   |     -         -     | 231       241       251    |    -    |  271       281  
                                                                                                            83    89                                                                                                                 205                   227                          256       266                 


Chain D from PDB  Type:PROTEIN  Length:250
 aligned with NADE_BACAN | Q81RP3 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:282
                                                                                                                                                                                                                                                                                                         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 d2pzbd_ D: NH3-dependent NAD+-synthetase                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2pzbD00 D:1-282 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhh....eeeeee.....----hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhh..................hhhhhhhhhhhh..hhhhhh---------------------.hhhhhhhhhh....hhhhhhhhhhhhhhh-------hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pzb D   1 MTLQEQIMKALHVQPVIDPKAEIRKRVDFLKDYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVEEIRNEGGNATFIAVRLPYKV----DDAQLALQFIQADQSVAFDIASTVDAFSNQYENLLDESLTDFNKGNVKARIRMVTQYAIGGQKGLLVIGTDHAAEAVTGFFTKFGDGGADLLPLTGLTKRQGRALLQELGADERLYL---------------------ITYDQLDDYLEGKTVPADVAEKIEKRYTVS-------ASMFDDWWKLAAALEHHHH 282
                                    10        20        30        40        50        60        70        80   |    90       100       110       120       130       140       150       160       170       180       190       200    |    -         -      |230       240       250     |   -   |   270       280  
                                                                                                              84   89                                                                                                                 205                   227                          256     264
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PZB)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  2pzb
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  NADE_BACAN | Q81RP3
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2pz8 THE SAME PROTEIN COMPLEXED WITH AMP-CPP.
2pza THE SAME PROTEIN COMPLEXED WITH AMP & PPI.