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(-) Description

Title :  CRYSTAL STRUCTURE OF PANTOTHENATE SYNTHETASE FROM STAPHYLOCOCCUS AUREUS
 
Authors :  A. Satoh, S. Konishi, H. Tamura, H. G. Stickland, H. M. Whitney, A. G. Smi H. Matsumura, T. Inoue
Date :  19 Mar 10  (Deposition) - 21 Jul 10  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pantothenate Synthetase, Open/Close Mechanism, Atp-Dependent Enzyme, Atp-Binding, Ligase, Nucleotide-Binding, Pantothenate Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Satoh, S. Konishi, H. Tamura, H. G. Stickland, H. M. Whitney, A. G. Smith, H. Matsumura, T. Inoue
Substrate-Induced Closing Of The Active Site Revealed By Th Crystal Structure Of Pantothenate Synthetase From Staphylococcus Aureus.
Biochemistry V. 49 6400 2010
PubMed-ID: 20568730  |  Reference-DOI: 10.1021/BI1004206

(-) Compounds

Molecule 1 - PANTOTHENATE SYNTHETASE
    Chains: A, B
    EC Number: 6.3.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD-TF
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PANC, SAOUHSC_02918
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 93061
    Strain: NCTC 8325
    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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3AG5)

(-) Sites  (0, 0)

(no "Site" information available for 3AG5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AG5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:248 -Pro A:249
2Tyr B:248 -Pro B:249

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AG5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AG5)

(-) Exons   (0, 0)

(no "Exon" information available for 3AG5)

(-) 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:278
 aligned with PANC_STAA8 | Q2FV22 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:283
                                    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   
           PANC_STAA8     1 MTKLITTVKEMQHIVKAAKRSGTTIGFIPTMGALHDGHLTMVRESVSTNDITIVSVFVNPLQFGPNEDFDAYPRQIDKDLELVSEVGADIVFHPAVEDMYPGELGIDVKVGPLADVLEGAKRPGHFDGVVTVVNKLFNIVMPDYAYFGKKDAQQLAIVEQMVKDFNHAVEIIGIDIVREADGLAKSSRNVYLTEQERQEAVHLSKSLLLAQALYQDGERQSKVIIDRVTEYLESHISERIEEVAVYSYPQLVEQHEITGRIFISLAVKFSKARLIDNIIIGAE 283
               SCOP domains d3ag5a_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.eeeeee..hhhhh.-----.....hhhhhhhhhhh....eee..hhhhhh.....eeeee.hhhh..hhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ag5 A   1 MTKLITTVKEMQHIVKAAKRSGTTIGFIPTMGALHDGHLTMVRESVSTNDITIVSVFVNPLQFG-----DAYPRQIDKDLELVSEVGADIVFHPAVEDMYPGELGIDVKVGPLADVLEGAKRPGHFDGVVTVVNKLFNIVMPDYAYFGKKDAQQLAIVEQMVKDFNHAVEIIGIDIVREADGLAKSSRNVYLTEQERQEAVHLSKSLLLAQALYQDGERQSKVIIDRVTEYLESHISERIEEVAVYSYPQLVEQHEITGRIFISLAVKFSKARLIDNIIIGAE 283
                                    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   
                                                                                          64    70                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:279
 aligned with PANC_STAA8 | Q2FV22 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:283
                                    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   
           PANC_STAA8     1 MTKLITTVKEMQHIVKAAKRSGTTIGFIPTMGALHDGHLTMVRESVSTNDITIVSVFVNPLQFGPNEDFDAYPRQIDKDLELVSEVGADIVFHPAVEDMYPGELGIDVKVGPLADVLEGAKRPGHFDGVVTVVNKLFNIVMPDYAYFGKKDAQQLAIVEQMVKDFNHAVEIIGIDIVREADGLAKSSRNVYLTEQERQEAVHLSKSLLLAQALYQDGERQSKVIIDRVTEYLESHISERIEEVAVYSYPQLVEQHEITGRIFISLAVKFSKARLIDNIIIGAE 283
               SCOP domains d3ag5b_ B: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhh..eeeeee..hhhhh----.......hhhhhhhhhhh....eee..hhhhhh.....eeeee.hhhh........hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...eeeeeeee.............eeeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ag5 B   1 MTKLITTVKEMQHIVKAAKRSGTTIGFIPTMGALHDGHLTMVRESVSTNDITIVSVFVNPLQF----DFDAYPRQIDKDLELVSEVGADIVFHPAVEDMYPGELGIDVKVGPLADVLEGAKRPGHFDGVVTVVNKLFNIVMPDYAYFGKKDAQQLAIVEQMVKDFNHAVEIIGIDIVREADGLAKSSRNVYLTEQERQEAVHLSKSLLLAQALYQDGERQSKVIIDRVTEYLESHISERIEEVAVYSYPQLVEQHEITGRIFISLAVKFSKARLIDNIIIGAE 283
                                    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   
                                                                                         63   68
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AG5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AG5)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PANC_STAA8 | Q2FV22)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.
biological process
    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.
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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  Cis Peptide Bonds
    Tyr A:248 - Pro A:249   [ RasMol ]  
    Tyr B:248 - Pro B:249   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PANC_STAA8 | Q2FV22: 3ag6

(-) Related Entries Specified in the PDB File

3ag6