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

(-) Description

Title :  CRYSTAL STRUCTURE OF A BIFUNCTIONAL NMN ADENYLYLTRANSFERASE/ADP RIBOSE PYROPHOSPHATASE FROM FRANCISELLA TULARENSIS
 
Authors :  N. Huang, L. Sorci, X. Zhang, C. Brautigan, X. Li, N. Raffaelli, N. Grishin, A. Osterman, H. Zhang
Date :  04 Sep 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 Domain Protein, Nucleotidyltransferase, Hydrolase, Transferase (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 Strain: BL21
    Expression System Taxid: 511693
    Gene: NADM
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. TULARENSIS
    Organism Taxid: 119856
    Strain: SUBSP. TULARENSIS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MG6Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:234 , GLY B:235 , GLU B:250 , GLU B:254 , ASP B:308 , HOH B:357 , HOH B:358BINDING SITE FOR RESIDUE MG B 348
2AC2SOFTWAREGLU B:250 , HOH B:354 , HOH B:355 , HOH B:356 , HOH B:386BINDING SITE FOR RESIDUE MG B 349
3AC3SOFTWAREGLU B:250 , GLU B:254 , ASP B:308 , HOH B:353BINDING SITE FOR RESIDUE MG B 350
4AC4SOFTWAREASP B:308 , HOH B:386 , HOH B:461BINDING SITE FOR RESIDUE CL B 351
5AC5SOFTWARELYS B:46 , ARG B:142 , GLN B:143BINDING SITE FOR RESIDUE CL B 352
6AC6SOFTWAREGLY A:234 , GLY A:235 , GLU A:254 , ASP A:308 , HOH A:356 , HOH A:427BINDING SITE FOR RESIDUE MG A 348
7AC7SOFTWAREGLU A:250 , HOH A:352 , HOH A:353 , HOH A:354 , HOH A:357BINDING SITE FOR RESIDUE MG A 349
8AC8SOFTWAREGLU A:250 , GLU A:254 , ASP A:308 , HOH A:357 , HOH A:388BINDING SITE FOR RESIDUE MG A 350
9AC9SOFTWAREGLY A:235 , ASP A:308 , HOH A:355 , HOH A:357 , HOH A:447BINDING SITE FOR RESIDUE CL A 351

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gln B:12 -Pro B:13
2Asp B:131 -Asn B:132
3His B:224 -Pro B:225
4Gly B:344 -Lys B:345
5Gln A:12 -Pro A:13
6Ala A:65 -Gly A:66
7His A:224 -Pro A:225
8Cys A:343 -Gly A:344

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R5W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R5W)

(-) Exons   (0, 0)

(no "Exon" information available for 2R5W)

(-) 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: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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhheeeeeeee.............hhhhhhhhhhhhhhh.......eeeee......hhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhh...eeee.......hhhhhhhhhh...............hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee..eeeeeee........ee..eee.....hhhhhhhhhhhhhhh...hhhhhhhheeeeeee..........eeeeeeeeee..............eeeeeeee.hhhhhhh......hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r5w A   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    


Chain B from PDB  Type:PROTEIN  Length:345
 aligned with Q5NHR1_FRATT | Q5NHR1 from UniProtKB/TrEMBL  Length:347

    Alignment length:345
                                    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 MYDISVFIGRFQPFHKGHLHNIIIALQNSKKVIINIGSCFNTPNIKNPFSFEQRKQMIESDLQVAGIDLDTVVIEPLADYFYQEQKWQDELRKNVYKHAKNNNSIAIVGHIKDSSSYYIRSFPEWDYIGVDNYKNFNATEFRQKFYNGIISKQYMCSNDPKLGTYNFLTKFMDTQVYQDLVAENNYVIEYKRLWLKAPFKPNFVTVDALVIVNDHILMVQRKAHPGKDLWALPGGFLECDETIAQAIIRELFEETNINLTHEQLAIAKRCEKVFDYPDRSVRGRTISHVGLFVFDQWPSLPEINAADDAKDVKWISLGSNIKNICDRMLEDHYQIITILLEECGK 345
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----CTP_transf_2-2r5wB01 B:6-122                                                                                         --------------------------------------------------------------------------------NUDIX-2r5wB03 B:203-339                                                                                                                  ------ Pfam domains (1)
           Pfam domains (2) -----CTP_transf_2-2r5wB02 B:6-122                                                                                         --------------------------------------------------------------------------------NUDIX-2r5wB04 B:203-339                                                                                                                  ------ Pfam domains (2)
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhh.eeeeeeeeeee..........hhhhhhhhhhhhhhhh..hhh.eeeeeee....hhhhhhhhhhhhhhh.......eee......hhhhhhhhh...ee.........hhhhhhhhhhh...hhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeee..eeeeeee........ee..eee.....hhhhhhhhhhhhhhh...hhhhhhhheeeeeee.........eeeeeeeeeee..............eeeeeeee.hhhhhh.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r5w B   1 MYDISVFIGRFQPFHKGHLHNIIIALQNSKKVIINIGSCFNTPNIKNPFSFEQRKQMIESDLQVAGIDLDTVVIEPLADYFYQEQKWQDELRKNVYKHAKNNNSIAIVGHIKDSSSYYIRSFPEWDYIGVDNYKNFNATEFRQKFYNGIISKQYMCSNDPKLGTYNFLTKFMDTQVYQDLVAENNYVIEYKRLWLKAPFKPNFVTVDALVIVNDHILMVQRKAHPGKDLWALPGGFLECDETIAQAIIRELFEETNINLTHEQLAIAKRCEKVFDYPDRSVRGRTISHVGLFVFDQWPSLPEINAADDAKDVKWISLGSNIKNICDRMLEDHYQIITILLEECGK 345
                                    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 2R5W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R5W)

(-) 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.

 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
    CL  [ 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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:65 - Gly A:66   [ RasMol ]  
    Asp B:131 - Asn B:132   [ RasMol ]  
    Cys A:343 - Gly A:344   [ RasMol ]  
    Gln A:12 - Pro A:13   [ RasMol ]  
    Gln B:12 - Pro B:13   [ RasMol ]  
    Gly B:344 - Lys B:345   [ RasMol ]  
    His A:224 - Pro A:225   [ RasMol ]  
    His B:224 - Pro B:225   [ RasMol ]  
 

(-) 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
  2r5w
    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
  Q5NHR1_FRATT | Q5NHR1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  3.6.1.-
    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
  Q5NHR1_FRATT | Q5NHR1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5NHR1_FRATT | Q5NHR1: 2qjt

(-) Related Entries Specified in the PDB File

2qjt THE SAME PROTEIN COMPLEXED WITH AMP AND MANGANESE ION