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(-) Description

Title :  THE CRYSTAL STRUCTURE OF PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE FROM THERMUS THERMOPHILUS IN COMPLEX WITH 4'-PHOSPHOPANTETHEINE
 
Authors :  H. Takahashi, E. Inagaki, M. Miyano, T. H. Tahirov
Date :  13 Feb 03  (Deposition) - 13 Mar 03  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Coenzyme A Biosynthesis, Transferase, Nucleotidyltransferase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Takahashi, E. Inagaki, Y. Fujimoto, C. Kuroishi, Y. Nodake, Y. Nakamura, F. Arisaka, K. Yutani, S. Kuramitsu, S. Yokoyama, M. Yamamoto, M. Miyano, T. H. Tahirov
Structure And Implications For The Thermal Stability Of Phosphopantetheine Adenylyltransferase From Thermus Thermophilus.
Acta Crystallogr. , Sect. D V. 60 97 2004
PubMed-ID: 14684898  |  Reference-DOI: 10.1107/S0907444903025319

(-) Compounds

Molecule 1 - PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
    Chains: A
    EC Number: 2.7.7.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: PPAT

 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, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1PNS1Ligand/Ion4'-PHOSPHOPANTETHEINE
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1PNS6Ligand/Ion4'-PHOSPHOPANTETHEINE
2SO418Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:104 , ARG A:107 , GLN A:108 , ALA A:121 , THR A:122 , HOH A:2124 , HOH A:2157BINDING SITE FOR RESIDUE SO4 A1162
2AC2SOFTWAREHIS A:16 , ARG A:91 , SER A:128 , SER A:129 , HOH A:2021 , HOH A:2158 , HOH A:2159 , HOH A:2160BINDING SITE FOR RESIDUE SO4 A1163
3AC3SOFTWAREGLN A:84 , TYR A:110 , HOH A:2115 , HOH A:2161 , HOH A:2162BINDING SITE FOR RESIDUE SO4 A1164
4AC4SOFTWAREPRO A:6 , GLY A:7 , SER A:8 , LEU A:35 , GLY A:72 , LEU A:73 , LEU A:74 , ASN A:106 , MET A:131 , GLU A:134 , HOH A:2133 , HOH A:2151 , HOH A:2152 , HOH A:2153 , HOH A:2154 , HOH A:2155 , HOH A:2156BINDING SITE FOR RESIDUE PNS A1161

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OD6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp A:10 -Pro A:11

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OD6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OD6)

(-) Exons   (0, 0)

(no "Exon" information available for 1OD6)

(-) 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:155
 aligned with COAD_THET8 | Q5SJS9 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
           COAD_THET8     1 MHVVYPGSFDPLTNGHLDVIQRASRLFEKVTVAVLENPSKRGQYLFSAEERLAIIREATAHLANVEAATFSGLLVDFVRRVGAQAIVKGLRAVSDYEYELQMAHLNRQLYPGLETLFILAATRYSFVSSTMVKEIARYGGDVSKLVPPATLRALKAKLGQ 160
               SCOP domains d1od6a_ A: Phosphopantetheine adenyly     ltransferase                                                                                                           SCOP domains
               CATH domains 1od6A00 A:1-160 Tyrosyl-Transfer RNA      Synthetase , subunit E, domain 1                                                                                       CATH domains
               Pfam domains ---CTP_transf_2-1od6A01 A:4-135                                                                                                        ------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhh.eeeeeee..-----....hhhhhhhhhhhhh.....eeeeee..hhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh...eeeeee.hhhhh..hhhhhhhhhhh........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1od6 A   1 MHVVYPGSFDPLTNGHLDVIQRASRLFEKVTVAVLEN-----QYLFSAEERLAIIREATAHLANVEAATFSGLLVDFVRRVGAQAIVKGLRAVSDYEYELQMAHLNRQLYPGLETLFILAATRYSFVSSTMVKEIARYGGDVSKLVPPATLRALKAKLGQ 160
                                    10        20        30      |  -  |     50        60        70        80        90       100       110       120       130       140       150       160
                                                               37    43
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (COAD_THET8 | Q5SJS9)
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: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:0004595    pantetheine-phosphate adenylyltransferase activity    Catalysis of the reaction: ATP + pantetheine 4'-phosphate = 3'-dephospho-CoA + diphosphate.
    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.
    GO:0015937    coenzyme A biosynthetic process    The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1b6t PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH 3'- DEPHOSPHO-COA FROM ESCHERICHIA COLI
1gn8 PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH MN2+ATP FROM ESCHERICHIA COLI
1h1t PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH COENZYME A FROM ESCHERICHIA COLI
1qjc PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE FROM ESCHERICHIA COLI