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(-) Description

Title :  STRUCTURAL AND SUBSTRATE-BINDING STUDIES OF PANTOTHENATE SYNTHENATE (PS)PROVIDE INSIGHTS INTO HOMOTROPIC INHIBITION BY PANTOATE IN PS'S
 
Authors :  K. S. Chakrabarti, K. G. Thakur, B. Gopal, S. P. Sarma
Date :  30 Mar 09  (Deposition) - 09 Feb 10  (Release) - 09 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pantothenate Biosynthesis, Substrate Binding, Competitive Inhibition, Rossmann Fold, Non-Canonical Pantoate Binding- Site, Atp-Binding, Cytoplasm, Ligase, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. S. Chakrabarti, K. G. Thakur, B. Gopal, S. P. Sarma
X-Ray Crystallographic And Nmr Studies Of Pantothenate Synthetase Provide Insights Into The Mechanism Of Homotropic Inhibition By Pantoate
Febs J. V. 277 697 2010
PubMed-ID: 20059543  |  Reference-DOI: 10.1111/J.1742-4658.2009.07515.X

(-) Compounds

Molecule 1 - PANTOTHENATE SYNTHETASE
    Chains: A, B
    EC Number: 6.3.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL-21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN
    Gene: PANC
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: PS, PANTOATE--BETA-ALANINE LIGASE, PANTOATE- ACTIVATING ENZYME

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1PAF3Ligand/IonPANTOATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:28 , THR A:29 , MET A:30 , GLN A:61 , ILE A:133 , GLN A:155 , HOH A:185 , HOH A:262 , HOH A:300 , HOH A:370BINDING SITE FOR RESIDUE PAF A 177
2AC2SOFTWAREGLY A:36 , LYS A:39 , GLY A:149 , LYS A:151 , HOH A:221 , HOH A:262 , HOH A:327 , HOH A:339 , HOH A:374BINDING SITE FOR RESIDUE PAF A 178
3AC3SOFTWAREPRO B:28 , THR B:29 , GLN B:61 , ILE B:133 , GLN B:155 , HOH B:214BINDING SITE FOR RESIDUE PAF B 177

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GUZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GUZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GUZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GUZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3GUZ)

(-) 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:165
 aligned with PANC_ECOLI | P31663 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:176
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      
           PANC_ECOLI     1 MLIIETLPLLRQQIRRLRMEGKRVALVPTMGNLHDGHMKLVDEAKARADVVVVSIFVNPMQFDRPEDLARYPRTLQEDCEKLNKRKVDLVFAPSVKEIYPNGTETHTYVDVPGLSTMLEGASRPGHFRGVSTIVSKLFNLVQPDIACFGEKDFQQLALIRKMVADMGFDIEIVGVP 176
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh..eeeeee..hhhhh.hhhhhhhh..hhhhhhhhhhhh...eee..hhhhhh........eee...-----------hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3guz A   1 MLIIETLPLLRQQIRRLRMEGKRVALVPTMGNLHDGHMKLVDEAKARADVVAVSIFVNPMQFDRPEDLARYPRTLQEDCEKLNKRKVDLVFAPSVKEIYPNGTETHTYVDVPG-----------GHFRGVSTIVSKLFNLVQPDIACFGEKDFQQLALIRKMVADMGFDIEIVGVP 176
                                    10        20        30        40        50        60        70        80        90       100       110  |      -    |  130       140       150       160       170      
                                                                                                                                          113         125                                                   


Chain B from PDB  Type:PROTEIN  Length:167
 aligned with PANC_ECOLI | P31663 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:176
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      
           PANC_ECOLI     1 MLIIETLPLLRQQIRRLRMEGKRVALVPTMGNLHDGHMKLVDEAKARADVVVVSIFVNPMQFDRPEDLARYPRTLQEDCEKLNKRKVDLVFAPSVKEIYPNGTETHTYVDVPGLSTMLEGASRPGHFRGVSTIVSKLFNLVQPDIACFGEKDFQQLALIRKMVADMGFDIEIVGVP 176
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.eeeeee..hhhhh.hhhhhhhh..hhhhhhhhhhhh...eee..hhhhhh........eee...---------..hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3guz B   1 MLIIETLPLLRQQIRRLRMEGKRVALVPTMGNLHDGHMKLVDEAKARADVVAVSIFVNPMQFDRPEDLARYPRTLQEDCEKLNKRKVDLVFAPSVKEIYPNGTETHTYVDVPG---------RPGHFRGVSTIVSKLFNLVQPDIACFGEKDFQQLALIRKMVADMGFDIEIVGVP 176
                                    10        20        30        40        50        60        70        80        90       100       110  |      -  |    130       140       150       160       170      
                                                                                                                                          113       123
   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 3GUZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GUZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GUZ)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PANC_ECOLI | P31663)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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: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:0004592    pantoate-beta-alanine ligase activity    Catalysis of the reaction: ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0015940    pantothenate biosynthetic process    The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
    GO:0033317    pantothenate biosynthetic process from valine    The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid, from other compounds, including valine.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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        PANC_ECOLI | P31663: 1iho

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