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(-) Description

Title :  CRYSTAL STRUCTURE OF A BIFUNCTIONAL NMN ADENYLYLTRANSFERASE/ADP RIBOSE PYROPHOSPHATASE COMPLEXED WITH AMP AND MN ION FROM FRANCISELLA TULARENSIS
 
Authors :  N. Huang, L. Sorci, X. Zhang, C. Brautigan, N. Raffaelli, G. Magni, N. V. Grishin, A. Osterman, H. Zhang
Date :  09 Jul 07  (Deposition) - 04 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Two Individual Domains, Transferase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Huang, L. Sorci, X. Zhang, C. A. Brautigam, X. Li, N. Raffaelli, G. Magni, N. V. Grishin, A. L. Osterman, H. Zhang
Bifunctional Nmn Adenylyltransferase/Adp-Ribose Pyrophosphatase: Structure And Function In Bacterial Nad Metabolism.
Structure V. 16 196 2008
PubMed-ID: 18275811  |  Reference-DOI: 10.1016/J.STR.2007.11.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NICOTINAMIDE-NUCLEOTIDE ADENYLYLTRANSFERASE
    Chains: B, A
    EC Number: 2.7.7.1, 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: GST PARALLEL
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: NADM
    Organism Scientific: FRANCISELLA TULARENSIS
    Organism Taxid: 263

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2MN9Ligand/IonMANGANESE (II) ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:234 , GLU A:254 , ASP A:308 , HOH A:693 , HOH A:694BINDING SITE FOR RESIDUE MN A 501
02AC2SOFTWAREGLN A:175 , GLN A:178 , HOH A:679 , HOH A:736BINDING SITE FOR RESIDUE MN A 502
03AC3SOFTWAREGLU A:250 , GLU A:254 , ASP A:308 , HOH A:710 , HOH A:711BINDING SITE FOR RESIDUE MN A 503
04AC4SOFTWAREGLU A:250 , HOH A:702 , HOH A:703 , HOH A:704 , HOH A:711BINDING SITE FOR RESIDUE MN A 504
05AC5SOFTWAREGLU B:250 , HOH B:675 , HOH B:676 , HOH B:677 , HOH B:687BINDING SITE FOR RESIDUE MN B 505
06AC6SOFTWAREGLU B:250 , GLU B:254 , ASP B:307 , ASP B:308 , HOH B:686 , HOH B:687BINDING SITE FOR RESIDUE MN B 506
07AC7SOFTWAREGLY B:234 , GLU B:254 , ASP B:308 , HOH B:684 , HOH B:685BINDING SITE FOR RESIDUE MN B 507
08AC8SOFTWAREHIS A:215 , HOH A:783BINDING SITE FOR RESIDUE MN A 508
09AC9SOFTWAREHIS B:215 , HOH B:795 , HOH B:796BINDING SITE FOR RESIDUE MN B 509
10BC1SOFTWARETYR A:190 , TRP A:194 , PHE A:203 , GLY A:234 , GLY A:235 , PHE A:236 , GLU A:250 , GLU A:254 , ASP A:308 , HOH A:693 , HOH A:700 , HOH A:702 , HOH A:711 , PHE B:199BINDING SITE FOR RESIDUE AMP A 601
11BC2SOFTWAREPHE A:199 , TYR B:190 , PHE B:203 , GLY B:234 , GLY B:235 , PHE B:236 , GLU B:250 , GLU B:254 , ASP B:308 , HOH B:677 , HOH B:678 , HOH B:680 , HOH B:684 , HOH B:687 , HOH B:743BINDING SITE FOR RESIDUE AMP B 602

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:270 -A:343
2B:270 -B:343

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Gln B:12 -Pro B:13
2His B:224 -Pro B:225
3Gln A:12 -Pro A:13
4Ala A:65 -Gly A:66
5Gly A:66 -Ile A:67
6His A:224 -Pro A:225
7Cys A:343 -Gly A:344

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QJT)

(-) 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:340
 aligned with Q5NHR1_FRATT | Q5NHR1 from UniProtKB/TrEMBL  Length:347

    Alignment length:344
                                    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       290       300       310       320       330       340    
         Q5NHR1_FRATT     1 MYDISVFIGRFQPFHKGHLHNIIIALQNSKKVIINIGSCFNTPNIKNPFSFEQRKQMIESDLQVAGIDLDTVVIEPLADYFYQEQKWQDELRKNVYKHAKNNNSIAIVGHIKDSSSYYIRSFPEWDYIGVDNYKNFNATEFRQKFYNGIISKQYMCSNDPKLGTYNFLTKFMDTQVYQDLVAENNYVIEYKRLWLKAPFKPNFVTVDALVIVNDHILMVQRKAHPGKDLWALPGGFLECDETIAQAIIRELFEETNINLTHEQLAIAKRCEKVFDYPDRSVRGRTISHVGLFVFDQWPSLPEINAADDAKDVKWISLGSNIKNICDRMLEDHYQIITILLEECG 344
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhh.eeeeeeeeeee..........hhhhhhhhhhhhhh....hhh.eeeeeee....hhhhhhhhhhhhhhh.......eeeee----hhhhhhhhh...eeee.......hhhhhhhhhh................hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh........eeeeeeeeeee..eeeeeee........ee..eee.....hhhhhhhhhhhhhhh...hhhhhhhheeeeeee.........eeeeeeeeeee..............eeeeeeee.hhhhhh.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qjt A   1 MYDISVFIGRFQPFHKGHLHNIIIALQNSKKVIINIGSCFNTPNIKNPFSFEQRKQMIESDLQVAGIDLDTVVIEPLADYFYQEQKWQDELRKNVYKHAKNNNSIAIVG----SSSYYIRSFPEWDYIGVDNYKNFNATEFRQKFYNGIISKQYMCSNDPKLGTYNFLTKFMDTQVYQDLVAENNYVIEYKRLWLKAPFKPNFVTVDALVIVNDHILMVQRKAHPGKDLWALPGGFLECDETIAQAIIRELFEETNINLTHEQLAIAKRCEKVFDYPDRSVRGRTISHVGLFVFDQWPSLPEINAADDAKDVKWISLGSNIKNICDRMLEDHYQIITILLEECG 344
                                    10        20        30        40        50        60        70        80        90       100        |-   |   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
                                                                                                                                      109  114                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:344
 aligned with Q5NHR1_FRATT | Q5NHR1 from UniProtKB/TrEMBL  Length:347

    Alignment length:344
                                    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       290       300       310       320       330       340    
         Q5NHR1_FRATT     1 MYDISVFIGRFQPFHKGHLHNIIIALQNSKKVIINIGSCFNTPNIKNPFSFEQRKQMIESDLQVAGIDLDTVVIEPLADYFYQEQKWQDELRKNVYKHAKNNNSIAIVGHIKDSSSYYIRSFPEWDYIGVDNYKNFNATEFRQKFYNGIISKQYMCSNDPKLGTYNFLTKFMDTQVYQDLVAENNYVIEYKRLWLKAPFKPNFVTVDALVIVNDHILMVQRKAHPGKDLWALPGGFLECDETIAQAIIRELFEETNINLTHEQLAIAKRCEKVFDYPDRSVRGRTISHVGLFVFDQWPSLPEINAADDAKDVKWISLGSNIKNICDRMLEDHYQIITILLEECG 344
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----CTP_transf_2-2qjtB01 B:6-122                                                                                         --------------------------------------------------------------------------------NUDIX-2qjtB03 B:203-339                                                                                                                  ----- Pfam domains (1)
           Pfam domains (2) -----CTP_transf_2-2qjtB02 B:6-122                                                                                         --------------------------------------------------------------------------------NUDIX-2qjtB04 B:203-339                                                                                                                  ----- Pfam domains (2)
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhheeeeeeeeeee..........hhhhhhhhhhhhhhhh..hhh.eeeeeee....hhhhhhhhhhhhhh........eee......hhhhhhhhh...ee.........hhhhhhhhhhh...hhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeee..eeeeeee........ee..eee.....hhhhhhhhhhhhhhh...hhhhhhhheeeeeee.........eeeeeeeeeee..............eeeeeeee.hhhhhhh......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qjt B   1 MYDISVFIGRFQPFHKGHLHNIIIALQNSKKVIINIGSCFNTPNIKNPFSFEQRKQMIESDLQVAGIDLDTVVIEPLADYFYQEQKWQDELRKNVYKHAKNNNSIAIVGHIKDSSSYYIRSFPEWDYIGVDNYKNFNATEFRQKFYNGIISKQYMCSNDPKLGTYNFLTKFMDTQVYQDLVAENNYVIEYKRLWLKAPFKPNFVTVDALVIVNDHILMVQRKAHPGKDLWALPGGFLECDETIAQAIIRELFEETNINLTHEQLAIAKRCEKVFDYPDRSVRGRTISHVGLFVFDQWPSLPEINAADDAKDVKWISLGSNIKNICDRMLEDHYQIITILLEECG 344
                                    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       290       300       310       320       330       340
   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  (0, 0)

(no "SCOP Domain" information available for 2QJT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QJT)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5NHR1_FRATT | Q5NHR1)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000309    nicotinamide-nucleotide adenylyltransferase activity    Catalysis of the reaction: ATP + nicotinamide nucleotide = diphosphate + NAD+.
    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.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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  2qjt
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 Related Entries

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UniProtKB/TrEMBL
        Q5NHR1_FRATT | Q5NHR1: 2r5w

(-) Related Entries Specified in the PDB File

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