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(-) Description

Title :  CRYSTAL STRUCTURE OF A NICOTINATE PHOSPHORIBOSYLTRANSFERASE FROM THERMOPLASMA ACIDOPHILUM WITH NICOTINATE MONONUCLEOTIDE
 
Authors :  D. H. Shin, Berkeley Structural Genomics Center (Bsgc)
Date :  10 Feb 05  (Deposition) - 08 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Nicotinate Phosphoribosyltransferase, Type Ii Phosphoribosyltransferase, Zinc-Knuckle Motif, Structural Genomics, Psi, Protein Structure Initiative, Berkeley Structural Genomics Center, Bsgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Shin, N. Oganesyan, J. Jancarik, H. Yokota, R. Kim, S. H. Kim
Crystal Structure Of A Nicotinate Phosphoribosyltransferase From Thermoplasma Acidophilum.
J. Biol. Chem. V. 280 18326 2005
PubMed-ID: 15753098  |  Reference-DOI: 10.1074/JBC.M501622200

(-) Compounds

Molecule 1 - NICOTINATE PHOSPHORIBOSYLTRANSFERASE FROM THERMOPLASMA ACIDOPHILUM
    Chains: A
    EC Number: 2.4.2.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834(DE3)/PSJS1244
    Expression System Taxid: 562
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 273075
    Strain: DSM 1728

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1NCN1Ligand/IonNICOTINATE MONONUCLEOTIDE
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1NCN6Ligand/IonNICOTINATE MONONUCLEOTIDE
2TRS6Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:19 , TYR A:21 , PHE A:138 , ARG A:141 , ARG A:142 , SER A:164 , GLY A:178 , THR A:179 , ARG A:235 , ASP A:237 , GLY A:272 , GLY A:292 , THR A:293 , HOH A:503 , HOH A:518 , HOH A:536BINDING SITE FOR RESIDUE NCN A 401
2AC2SOFTWARETHR A:50 , GLY A:118 , THR A:121 , LYS A:122 , LYS A:125 , LYS A:299 , HOH A:560BINDING SITE FOR RESIDUE TRS A 402

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:33 -A:100

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YTK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YTK)

(-) 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:389
 aligned with PNCB_THEAC | Q9HJ28 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:389
                                    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       350       360       370       380         
           PNCB_THEAC     1 MNVFNTASDEDIKKGLASDVYFERTISAIGDKCNDLRVAMEATVSGPLDTWINFTGLDEVLKLLEGLDVDLYAIPEGTILFPRDANGLPVPFIRVEGRYCDFGMYETAILGFICQASGISTKASKVRLAAGDSPFFSFGIRRMHPAISPMIDRSAYIGGADGVSGILGAKLIDQDPVGTMPHALSIMLGDEEAWKLTLENTKNGQKSVLLIDTYMDEKFAAIKIAEMFDKVDYIRLDTPSSRRGNFEALIREVRWELALRGRSDIKIMVSGGLDENTVKKLREAGAEAFGVGTSISSAKPFDFAMDIVEVNGKPETKRGKMSGRKNVLRCTSCHRIEVVPANVQEKTCICGGSMQNLLVKYLSHGKRTSEYPRPKEIRSRSMKELEYFK 389
               SCOP domains d1ytka1 A:1-119 Nicotinate phosphoribosyltransferase Ta1145                                                            d1ytka2 A:120-389 Nicotinate phosphoribosyltransferase Ta1145                                                                                                                                                                                                                  SCOP domains
               CATH domains 1ytkA01 A:1-110  [code=3.90.1170.20, no name defined]                                                         1ytkA02 A:111-300 Aldolase class I                                                                                                                                                            ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh.....hhhhhhhhhhhhhhhh.eeeeeeee.......ee..hhhhhhhhhh....eeee.....ee..........eeeeeeeehhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......eee.....hhhhhhhhhhh......eeee..hhhhh.hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhh..eeeehhhhhh.....eeeeeeee..ee..........eeeeee.....eeeee....eee.....eeee..eeeee..ee.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ytk A   1 MNVFNTASDEDIKKGLASDVYFERTISAIGDKCNDLRVAMEATVSGPLDTWINFTGLDEVLKLLEGLDVDLYAIPEGTILFPRDANGLPVPFIRVEGRYCDFGMYETAILGFICQASGISTKASKVRLAAGDSPFFSFGIRRMHPAISPMIDRSAYIGGADGVSGILGAKLIDQDPVGTMPHALSIMLGDEEAWKLTLENTKNGQKSVLLIDTYMDEKFAAIKIAEMFDKVDYIRLDTPSSRRGNFEALIREVRWELALRGRSDIKIMVSGGLDENTVKKLREAGAEAFGVGTSISSAKPFDFAMDIVEVNGKPETKRGKMSGRKNVLRCTSCHRIEVVPANVQEKTCICGGSMQNLLVKYLSHGKRTSEYPRPKEIRSRSMKELEYFK 389
                                    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       350       360       370       380
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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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (PNCB_THEAC | Q9HJ28)
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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004514    nicotinate-nucleotide diphosphorylase (carboxylating) activity    Catalysis of the reaction: CO(2) + diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H(+) + quinolinate.
    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: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.
    GO:0016763    transferase activity, transferring pentosyl groups    Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
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: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
        PNCB_THEAC | Q9HJ28: 1ytd 1yte 2i1o

(-) Related Entries Specified in the PDB File

1ytd NATIVE STRUCTURE
1yte PHOSPHORIBOSYLPYROPHOSPHATE BOUND STRUCTURE RELATED ID: BSGCAIR30619 RELATED DB: TARGETDB