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(-) Description

Title :  CRYSTAL STRUCTURE OF NICOTINIC ACID MONONUCLEOTIDE ADENYLYLTRANSFERASE FROM PSEUDOMONAS AERUGINOSA
 
Authors :  H. J. Yoon, H. L. Kim, B. Mikami, S. W. Suh
Date :  14 Feb 05  (Deposition) - 08 Nov 05  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Alpha/Beta Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Yoon, H. L. Kim, B. Mikami, S. W. Suh
Crystal Structure Of Nicotinic Acid Mononucleotide Adenylyltransferase From Pseudomonas Aeruginosa In Its Apo And Substrate-Complexed Forms Reveals A Fully Open Conformation
J. Mol. Biol. V. 351 258 2005
PubMed-ID: 16009375  |  Reference-DOI: 10.1016/J.JMB.2005.06.001

(-) Compounds

Molecule 1 - 'PROBABLE NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.7.7.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28B(+)
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NADD (PA4006)
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: NICOTINIC ACID MONONUCLEOTIDE ADENYLYLTRANSFERASE, NAMN AT, DEAMIDO-NAD+, PYROPHOSPHORYLASE, DEAMIDO-NAD+, DIPHOSPHORYLASE, NICOTINATE MONONUCLEOTIDE ADENYLYLTRANSFERASE, NAMN ADENYLYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2NCN4Ligand/IonNICOTINATE MONONUCLEOTIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:11 , PHE A:12 , HIS A:16 , HIS A:19 , SER A:178 , ALA A:179 , THR A:180 , HOH A:455BINDING SITE FOR RESIDUE CIT A 301
2AC2SOFTWAREASN A:40 , TYR A:84 , THR A:85 , ALA A:110 , TRP A:117 , HIS A:118 , HOH A:1174BINDING SITE FOR RESIDUE NCN A 302
3AC3SOFTWAREHIS B:16 , HIS B:19 , SER B:178 , ALA B:179 , THR B:180 , HOH B:497 , HOH B:515 , HOH B:532BINDING SITE FOR RESIDUE CIT B 1301
4AC4SOFTWAREASN B:40 , TYR B:84 , THR B:85 , TRP B:117 , HIS B:118 , HOH B:520 , HOH B:556 , HOH B:587BINDING SITE FOR RESIDUE NCN B 1302
5AC5SOFTWARETHR C:11 , PHE C:12 , ASP C:13 , HIS C:16 , HIS C:19 , SER C:178 , ALA C:179 , THR C:180 , HOH C:724 , HOH C:814 , HOH C:842 , HOH C:861BINDING SITE FOR RESIDUE CIT C 2301
6AC6SOFTWAREASN C:40 , TYR C:84 , THR C:85 , TRP C:117 , HIS C:118 , HOH C:712 , HOH C:751 , HOH C:778 , HOH C:827 , HOH C:1167BINDING SITE FOR RESIDUE NCN C 2302
7AC7SOFTWARETHR D:11 , PHE D:12 , HIS D:16 , HIS D:19 , SER D:178 , ALA D:179 , THR D:180 , HOH D:888 , HOH D:920 , HOH D:942 , HOH D:1035 , HOH D:1160BINDING SITE FOR RESIDUE CIT D 3301
8AC8SOFTWAREASN D:40 , TYR D:84 , THR D:85 , TRP D:117 , HIS D:118 , HOH D:945 , HOH D:970BINDING SITE FOR RESIDUE NCN D 3302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YUM)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp A:13 -Pro A:14
2Asp B:13 -Pro B:14
3Asp C:13 -Pro C:14
4Asp D:13 -Pro D:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YUM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YUM)

(-) Exons   (0, 0)

(no "Exon" information available for 1YUM)

(-) 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:212
 aligned with NADD_PSEAE | Q9HX21 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  
           NADD_PSEAE     2 GKRIGLFGGTFDPVHIGHMRSAVEMAEQFALDELRLLPNARPPHRETPQVSAAQRLAMVERAVAGVERLTVDPRELQRDKPSYTIDTLESVRAELAADDQLFMLIGWDAFCGLPTWHRWEALLDHCHIVVLQRPDADSEPPESLRDLLAARSVADPQALKGPGGQITFVWQTPLAVSATQIRALLGAGRSVRFLVPDAVLNYIEAHHLYRAP 213
               SCOP domains d1yuma_ A: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains 1yumA00 A:2-213 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhh..eeeeee...hhhhh....hhhhhhhhhhhhhh....eee.hhhhhh....hhhhhhhhhhhhh....eeeeeeehhhhhhhhhh.hhhhh....eeeeee........hhhhhhhhhhhh..hhhhh......eeeee......hhhhhhhhhhh........hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yum A   2 GKRIGLFGGTFDPVHIGHMRSAVEMAEQFALDELRLLPNARPPHRETPQVSAAQRLAMVERAVAGVERLTVDPRELQRDKPSYTIDTLESVRAELAADDQLFMLIGWDAFCGLPTWHRWEALLDHCHIVVLQRPDADSEPPESLRDLLAARSVADPQALKGPGGQITFVWQTPLAVSATQIRALLGAGRSVRFLVPDAVLNYIEAHHLYRAP 213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  


Chain B from PDB  Type:PROTEIN  Length:212
 aligned with NADD_PSEAE | Q9HX21 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  
           NADD_PSEAE     2 GKRIGLFGGTFDPVHIGHMRSAVEMAEQFALDELRLLPNARPPHRETPQVSAAQRLAMVERAVAGVERLTVDPRELQRDKPSYTIDTLESVRAELAADDQLFMLIGWDAFCGLPTWHRWEALLDHCHIVVLQRPDADSEPPESLRDLLAARSVADPQALKGPGGQITFVWQTPLAVSATQIRALLGAGRSVRFLVPDAVLNYIEAHHLYRAP 213
               SCOP domains d1yumb_ B: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains 1yumB00 B:2-213 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhh....hhhhhhhhhhhhhh....eee.hhhhh.....hhhhhhhhhh.......eeeeeeehhhhhhhhhh.hhhhhhhh.eeeeee........hhhhhhhhhhhh..hhhhh......eeeee......hhhhhhhhhhh........hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yum B   2 GKRIGLFGGTFDPVHIGHMRSAVEMAEQFALDELRLLPNARPPHRETPQVSAAQRLAMVERAVAGVERLTVDPRELQRDKPSYTIDTLESVRAELAADDQLFMLIGWDAFCGLPTWHRWEALLDHCHIVVLQRPDADSEPPESLRDLLAARSVADPQALKGPGGQITFVWQTPLAVSATQIRALLGAGRSVRFLVPDAVLNYIEAHHLYRAP 213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  


Chain C from PDB  Type:PROTEIN  Length:212
 aligned with NADD_PSEAE | Q9HX21 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  
           NADD_PSEAE     2 GKRIGLFGGTFDPVHIGHMRSAVEMAEQFALDELRLLPNARPPHRETPQVSAAQRLAMVERAVAGVERLTVDPRELQRDKPSYTIDTLESVRAELAADDQLFMLIGWDAFCGLPTWHRWEALLDHCHIVVLQRPDADSEPPESLRDLLAARSVADPQALKGPGGQITFVWQTPLAVSATQIRALLGAGRSVRFLVPDAVLNYIEAHHLYRAP 213
               SCOP domains d1yumc_ C: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains 1yumC00 C:2-213 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhh....hhhhhhhhhhhhhh....eee.hhhhhh....hhhhhhhhhhhhh....eeeeeeehhhhhhhhhh.hhhhhhhh.eeeeee........hhhhhhhhhhhh..hhhhh......eeeee......hhhhhhhhhhh........hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yum C   2 GKRIGLFGGTFDPVHIGHMRSAVEMAEQFALDELRLLPNARPPHRETPQVSAAQRLAMVERAVAGVERLTVDPRELQRDKPSYTIDTLESVRAELAADDQLFMLIGWDAFCGLPTWHRWEALLDHCHIVVLQRPDADSEPPESLRDLLAARSVADPQALKGPGGQITFVWQTPLAVSATQIRALLGAGRSVRFLVPDAVLNYIEAHHLYRAP 213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  


Chain D from PDB  Type:PROTEIN  Length:212
 aligned with NADD_PSEAE | Q9HX21 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  
           NADD_PSEAE     2 GKRIGLFGGTFDPVHIGHMRSAVEMAEQFALDELRLLPNARPPHRETPQVSAAQRLAMVERAVAGVERLTVDPRELQRDKPSYTIDTLESVRAELAADDQLFMLIGWDAFCGLPTWHRWEALLDHCHIVVLQRPDADSEPPESLRDLLAARSVADPQALKGPGGQITFVWQTPLAVSATQIRALLGAGRSVRFLVPDAVLNYIEAHHLYRAP 213
               SCOP domains d1yumd_ D: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains 1yumD00 D:2-213 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                CATH domains
           Pfam domains (1) -----CTP_transf_2-1yumD01 D:7-185                                                                                                                                                       ---------------------------- Pfam domains (1)
           Pfam domains (2) -----CTP_transf_2-1yumD02 D:7-185                                                                                                                                                       ---------------------------- Pfam domains (2)
           Pfam domains (3) -----CTP_transf_2-1yumD03 D:7-185                                                                                                                                                       ---------------------------- Pfam domains (3)
           Pfam domains (4) -----CTP_transf_2-1yumD04 D:7-185                                                                                                                                                       ---------------------------- Pfam domains (4)
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhh..eeeeee...hhhhh....hhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhh....eeeeeeehhhhhhhhhh.hhhhhhhh.eeeeee........hhhhhhhhhhhh.............eeeee......hhhhhhhhhhh........hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yum D   2 GKRIGLFGGTFDPVHIGHMRSAVEMAEQFALDELRLLPNARPPHRETPQVSAAQRLAMVERAVAGVERLTVDPRELQRDKPSYTIDTLESVRAELAADDQLFMLIGWDAFCGLPTWHRWEALLDHCHIVVLQRPDADSEPPESLRDLLAARSVADPQALKGPGGQITFVWQTPLAVSATQIRALLGAGRSVRFLVPDAVLNYIEAHHLYRAP 213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (NADD_PSEAE | Q9HX21)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0000309    nicotinamide-nucleotide adenylyltransferase activity    Catalysis of the reaction: ATP + nicotinamide nucleotide = diphosphate + NAD+.
    GO:0004515    nicotinate-nucleotide adenylyltransferase activity    Catalysis of the reaction: ATP + nicotinate ribonucleotide = diphosphate + deamido-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:0034628    'de novo' NAD biosynthetic process from aspartate    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of aspartate from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    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: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.
    GO:0019363    pyridine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NADD_PSEAE | Q9HX21: 1yul 1yun

(-) Related Entries Specified in the PDB File

1yul THA SAME PROTEIN WITH CITRIC ACID
1yun THA SAME PROTEIN WITH ADENOSINE-5'-TRIPHOSPHATE AND MG