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(-) Description

Title :  CRYSTAL STRUCTURE OF PANTOTHENATE SYNTHETASE FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH PANTOYL ADENYLATE
 
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 :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pantothenate Synthetase, 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  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2PAJ2Ligand/IonPANTOYL ADENYLATE
3PG48Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:29 , THR A:30 , MET A:31 , HIS A:35 , HIS A:38 , MET A:41 , GLN A:62 , VAL A:132 , PHE A:147 , GLY A:148 , ASP A:151 , GLN A:154 , ILE A:174 , ASP A:175 , ILE A:176 , VAL A:177 , LYS A:185 , HOH A:290 , HOH A:305 , HOH A:431 , HOH A:435 , HOH A:442 , HOH A:502BINDING SITE FOR RESIDUE PAJ A 501
02AC2SOFTWAREMET A:31 , GLN A:62 , ARG A:122 , HIS A:125 , ARG A:188 , HOH A:288 , HOH A:472BINDING SITE FOR RESIDUE ACY A 801
03AC3SOFTWARELYS A:9 , GLN A:12 , LYS A:16 , ALA B:168 , VAL B:169BINDING SITE FOR RESIDUE PG4 A 903
04AC4SOFTWAREGLU A:179 , ASN A:189 , GLU A:194 , ARG A:197 , GLN A:198BINDING SITE FOR RESIDUE PG4 A 905
05AC5SOFTWAREASP A:115 , HOH A:507BINDING SITE FOR RESIDUE PG4 A 907
06AC6SOFTWAREPRO B:29 , THR B:30 , MET B:31 , HIS B:35 , HIS B:38 , MET B:41 , GLN B:62 , VAL B:132 , PHE B:147 , GLY B:148 , LYS B:150 , ASP B:151 , GLN B:154 , ASP B:175 , ILE B:176 , VAL B:177 , LYS B:185 , HOH B:284 , HOH B:298 , HOH B:336 , HOH B:393 , HOH B:422 , ACY B:802BINDING SITE FOR RESIDUE PAJ B 502
07AC7SOFTWAREMET B:31 , GLN B:62 , ARG B:122 , HIS B:125 , ARG B:188 , HOH B:334 , HOH B:471 , PAJ B:502BINDING SITE FOR RESIDUE ACY B 802
08AC8SOFTWAREASP A:143 , ALA A:168 , LYS B:9 , GLN B:12 , LYS B:16 , HOH B:389BINDING SITE FOR RESIDUE PG4 B 901
09AC9SOFTWARELEU B:61 , PHE B:63 , GLY B:64 , PRO B:65BINDING SITE FOR RESIDUE PG4 B 904
10BC1SOFTWAREGLU B:179 , ASN B:189 , LEU B:192 , ARG B:197BINDING SITE FOR RESIDUE PG4 B 906
11BC2SOFTWAREARG B:178 , GLY B:182 , SER B:204 , LEU B:208 , ASN B:277 , ILE B:278 , HOH B:423BINDING SITE FOR RESIDUE PG4 B 908

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AG6)

(-) 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 3AG6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AG6)

(-) Exons   (0, 0)

(no "Exon" information available for 3AG6)

(-) 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:283
 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 d3ag6a_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh...eeeeee..hhhhh...........hhhhhhhhhhhhh..eee..hhhhhh.....eeeee.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeee.............eeeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ag6 A   1 MTKLITTVKEMQHIVKAAKRSGTTIGFIPTMGALHDGHLTMVRESVSTNDITIVSVFVNPLQFGPNEDFDAYPRQIDKDLELVSEVGADIVFHPAVEDMYPGELGIDVKVGPLADVLEGAKRPGHFDGVVTVVNKLFNIVMPDYAYFGKKDAQQLAIVEQMVKDFNHAVEIIGIDIVREADGLAKSSRNVYLTEQERQEAVHLSKSLLLAQALYQDGERQSKVIIDRVTEYLESHISERIEEVAVYSYPQLVEQHEITGRIFISLAVKFSKARLIDNIIIGAE 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   


Chain B from PDB  Type:PROTEIN  Length:283
 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 d3ag6b_ B: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhh...eeeeee..hhhhh...........hhhhhhhhhhhhh..eee..hhhhhh.....eeeee.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...........hhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....eeeeeeeee.............eeeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ag6 B   1 MTKLITTVKEMQHIVKAAKRSGTTIGFIPTMGALHDGHLTMVRESVSTNDITIVSVFVNPLQFGPNEDFDAYPRQIDKDLELVSEVGADIVFHPAVEDMYPGELGIDVKVGPLADVLEGAKRPGHFDGVVTVVNKLFNIVMPDYAYFGKKDAQQLAIVEQMVKDFNHAVEIIGIDIVREADGLAKSSRNVYLTEQERQEAVHLSKSLLLAQALYQDGERQSKVIIDRVTEYLESHISERIEEVAVYSYPQLVEQHEITGRIFISLAVKFSKARLIDNIIIGAE 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
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AG6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AG6)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        PANC_STAA8 | Q2FV22: 3ag5

(-) Related Entries Specified in the PDB File

3ag5 THE SAME PROTEIN IN APO FORM