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(-) Description

Title :  CRYSTAL STRUCTURE OF THE METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS SAR2676, A PANTOTHENATE SYNTHETASE.
 
Authors :  M. Oke, L. G. Carter, K. A. Johnson, H. Liu, S. A. Mcmahon, M. F. White, J. H. Naismith
Date :  24 Jan 10  (Deposition) - 21 Jul 10  (Release) - 21 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Atp-Binding, Nucleotide-Binding, Pantothenate Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Oke, L. G. Carter, K. A. Johnson, H. Liu, S. A. Mcmahon, X. Yan, M. Kerou, N. D. Weikart, N. Kadi, M. A. Sheikh, S. Schmelz, M. Dorward, M. Zawadzki, C. Cozens, H. Falconer, H. Powers, I. M. Overton, C. A. J. Van Niekerk, X. Peng, P. Patel, R. A. Garrett, D. Prangishvili C. H. Botting, P. J. Coote, D. T. F. Dryden, G. J. Barton, U. Schwarz-Linek, G. L. Challis, G. L. Taylor, M. F. White, J. H. Naismith
The Scottish Structural Proteomics Facility: Targets, Methods And Outputs.
J. Struct. Funct. Genom. V. 11 167 2010
PubMed-ID: 20419351  |  Reference-DOI: 10.1007/S10969-010-9090-Y
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PANTHOTHENATE SYNTHETASE
    Chains: A, B
    EC Number: 6.3.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 282458
    Strain: MRSA252
    Synonym: PANTOATE--BETA-ALANINE LIGASE, PANTOATE-ACTIVATING ENZYME, PS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1APC2Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:29 , THR A:30 , MET A:31 , HIS A:35 , HIS A:38 , MET A:41 , TYR A:72 , PHE A:147 , GLY A:148 , LYS A:150 , ASP A:151 , ASP A:175 , ILE A:176 , VAL A:177 , LYS A:185 , SER A:186 , SER A:187 , ARG A:188 , SO4 A:1284 , HOH A:2010BINDING SITE FOR RESIDUE APC A1283
2AC2SOFTWAREMET A:31 , GLN A:62 , ARG A:122 , HIS A:125 , ARG A:188 , APC A:1283 , HOH A:2048 , HOH A:2110BINDING SITE FOR RESIDUE SO4 A1284
3AC3SOFTWAREPRO B:29 , MET B:31 , HIS B:35 , HIS B:38 , MET B:41 , TYR B:72 , PHE B:147 , GLY B:148 , LYS B:150 , ASP B:151 , ASP B:175 , ILE B:176 , VAL B:177 , LYS B:185 , SER B:186 , SER B:187 , ARG B:188 , HOH B:2014 , HOH B:2087BINDING SITE FOR RESIDUE APC B1283

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X3F)

(-) 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 2X3F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X3F)

(-) Exons   (0, 0)

(no "Exon" information available for 2X3F)

(-) 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:281
 aligned with PANC_STAAR | Q6GDK5 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:281
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281 
           PANC_STAAR     2 TKLITTVKEMQHIVKAAKRSGTTIGFIPTMGALHDGHLTMVRESVSTNDITVVSVFVNPLQFGPNEDFDAYPRQIDKDLELVSEVGADIVFHPAVEDMYPGELGIDVKVGPLADVLEGAKRPGHFDGVVTVVNKLFNIVMPDYAYFGKKDAQQLAIVEQMVKDFNHAVEIIGIDIVREADGLAKSSRNVYLTEQERQEAVHLSKSLLLAQALYQDGERQSKVIIDKVTQYLESHISGRIEEVAVYSYPQLVEQHEITGRIFISLAVKFSKARLIDNIIIGA 282
               SCOP domains d2x3fa_ A: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -2x3fA01 A:3-178 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                           2x3fA02 A:179-278  [code=3.30.1300.10, no name defined]                                             ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh.eeeeee..hhhhh...........hhhhhhhhhhhh...eee..hhhhhh.....eeeee.hhhh.hhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....eeeeeeeee.............eeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x3f A   2 TKLITTVKEMQHIVKAAKRSGTTIGFIPTMGALHDGHLTMVRESVSTNDITVVSVFVNPLQFGPNEDFDAYPRQIDKDLELVSEVGADIVFHPAVEDMYPGELGIDVKVGPLADVLEGAKRPGHFDGVVTVVNKLFNIVMPDYAYFGKKDAQQLAIVEQMVKDFNHAVEIIGIDIVREADGLAKSSRNVYLTEQERQEAVHLSKSLLLAQALYQDGERQSKVIIDKVTQYLESHISGRIEEVAVYSYPQLVEQHEITGRIFISLAVKFSKARLIDNIIIGA 282
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281 


Chain B from PDB  Type:PROTEIN  Length:281
 aligned with PANC_STAAR | Q6GDK5 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:282
                                    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_STAAR     1 MTKLITTVKEMQHIVKAAKRSGTTIGFIPTMGALHDGHLTMVRESVSTNDITVVSVFVNPLQFGPNEDFDAYPRQIDKDLELVSEVGADIVFHPAVEDMYPGELGIDVKVGPLADVLEGAKRPGHFDGVVTVVNKLFNIVMPDYAYFGKKDAQQLAIVEQMVKDFNHAVEIIGIDIVREADGLAKSSRNVYLTEQERQEAVHLSKSLLLAQALYQDGERQSKVIIDKVTQYLESHISGRIEEVAVYSYPQLVEQHEITGRIFISLAVKFSKARLIDNIIIGA 282
               SCOP domains d2x3fb_ B: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains --2x3fB01 B:3-178 Tyrosyl-Transfer RNA Synthetase , subunit E, domain  1                                                                                                          2x3fB02 B:179-278  [code=3.30.1300.10, no name defined]                                             ---- CATH domains
           Pfam domains (1) -Pantoate_ligase-2x3fB01 B:2-280                                                                                                                                                                                                                                                        -- Pfam domains (1)
           Pfam domains (2) -Pantoate_ligase-2x3fB02 B:2-280                                                                                                                                                                                                                                                        -- Pfam domains (2)
         Sec.struct. author ..eee.hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh.eeeeee..hhhhh......-....hhhhhhhhhhhh...eee..hhhhhh.....eeeee.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....eeeeeeeee.............eeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x3f B   1 MTKLITTVKEMQHIVKAAKRSGTTIGFIPTMGALHDGHLTMVRESVSTNDITVVSVFVNPLQFGPNEDF-AYPRQIDKDLELVSEVGADIVFHPAVEDMYPGELGIDVKVGPLADVLEGAKRPGHFDGVVTVVNKLFNIVMPDYAYFGKKDAQQLAIVEQMVKDFNHAVEIIGIDIVREADGLAKSSRNVYLTEQERQEAVHLSKSLLLAQALYQDGERQSKVIIDKVTQYLESHISGRIEEVAVYSYPQLVEQHEITGRIFISLAVKFSKARLIDNIIIGA 282
                                    10        20        30        40        50        60        |-|       80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  
                                                                                               69 |                                                                                                                                                                                                                   
                                                                                                 71
   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  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PANC_STAAR | Q6GDK5)
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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