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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) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
    Chains: A, B
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:16 , SER B:178 , ALA B:179 , ATP B:1220BINDING SITE FOR RESIDUE MG B 230
2AC2SOFTWAREPHE A:8 , GLY A:9 , GLY A:10 , THR A:11 , PHE A:12 , ASP A:13 , HIS A:16 , GLY A:18 , HIS A:19 , SER A:22 , PRO A:174 , LEU A:175 , VAL A:177 , SER A:178 , ALA A:179 , THR A:180 , ARG A:183 , HOH A:398 , HOH A:416 , HOH A:425 , HOH A:521 , HOH A:556BINDING SITE FOR RESIDUE ATP A 223
3AC3SOFTWAREPHE B:8 , GLY B:9 , GLY B:10 , THR B:11 , PHE B:12 , HIS B:16 , GLY B:18 , HIS B:19 , SER B:22 , GLN B:172 , PRO B:174 , LEU B:175 , ALA B:179 , MG B:230 , HOH B:310 , HOH B:364 , HOH B:524BINDING SITE FOR RESIDUE ATP B 1220

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:13 -Pro A:14
2Asp B:13 -Pro B:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YUN)

(-) 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:210
 aligned with NADD_PSEAE | Q9HX21 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
           NADD_PSEAE     2 GKRIGLFGGTFDPVHIGHMRSAVEMAEQFALDELRLLPNARPPHRETPQVSAAQRLAMVERAVAGVERLTVDPRELQRDKPSYTIDTLESVRAELAADDQLFMLIGWDAFCGLPTWHRWEALLDHCHIVVLQRPDADSEPPESLRDLLAARSVADPQALKGPGGQITFVWQTPLAVSATQIRALLGAGRSVRFLVPDAVLNYIEAHHLYR 211
               SCOP domains d1yuna_ A: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains 1yunA00 A:2-211 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhh..eeeeee...hhhhh....hhhhhhhhhhhhhh....eee..hhhhh....hhhhhhhhhhhh.....eeeeeeehhhhhhhhhh.hhhhhhhhheeeeee........hhhhhhhhhhhh..hhhhh......eeeee......hhhhhhhhhhh........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yun A   2 GKRIGLFGGTFDPVHIGHMRSAVEMAEQFALDELRLLPNARPPHRETPQVSAAQRLAMVERAVAGVERLTVDPRELQRDKPSYTIDTLESVRAELAADDQLFMLIGWDAFCGLPTWHRWEALLDHCHIVVLQRPDADSEPPESLRDLLAARSVADPQALKGPGGQITFVWQTPLAVSATQIRALLGAGRSVRFLVPDAVLNYIEAHHLYR 211
                                    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:210
 aligned with NADD_PSEAE | Q9HX21 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
           NADD_PSEAE     2 GKRIGLFGGTFDPVHIGHMRSAVEMAEQFALDELRLLPNARPPHRETPQVSAAQRLAMVERAVAGVERLTVDPRELQRDKPSYTIDTLESVRAELAADDQLFMLIGWDAFCGLPTWHRWEALLDHCHIVVLQRPDADSEPPESLRDLLAARSVADPQALKGPGGQITFVWQTPLAVSATQIRALLGAGRSVRFLVPDAVLNYIEAHHLYR 211
               SCOP domains d1yunb_ B: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains 1yunB00 B:2-211 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........hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yun B   2 GKRIGLFGGTFDPVHIGHMRSAVEMAEQFALDELRLLPNARPPHRETPQVSAAQRLAMVERAVAGVERLTVDPRELQRDKPSYTIDTLESVRAELAADDQLFMLIGWDAFCGLPTWHRWEALLDHCHIVVLQRPDADSEPPESLRDLLAARSVADPQALKGPGGQITFVWQTPLAVSATQIRALLGAGRSVRFLVPDAVLNYIEAHHLYR 211
                                    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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YUN)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 1yum

(-) Related Entries Specified in the PDB File

1yul THA SAME PROTEIN WITH CITRIC ACID
1yum THA SAME PROTEIN WITH CITRIC ACID AND NICOTINATE MONONUCLEOTIDE