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(-) Description

Title :  PANTOTHENATE SYNTHETASE IN COMPLEX WITH RACEMATE (2S)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID AND (2R)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID
 
Authors :  H. L. Silvestre, T. L. Blundell, C. Abell, A. Ciulli
Date :  17 Jul 12  (Deposition) - 17 Jul 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Alpha Beta 3-Layer(Aba) Sandwich Rossmann Fold, Ligase, Atp Binding Pantoate Binding Beta-Alanine Binding, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Silvestre, T. L. Blundell, C. Abell, A. Ciulli
Integrated Biophysical Approach To Fragment Screening And Validation For Fragment-Based Lead Discovery.
Proc. Natl. Acad. Sci. Usa V. 110 12984 2013
PubMed-ID: 23872845  |  Reference-DOI: 10.1073/PNAS.1304045110

(-) Compounds

Molecule 1 - PANTOTHENATE SYNTHETASE
    Chains: A, B
    EC Number: 6.3.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30B
    Expression System Strain: ROSETTA2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MT3707, MTCY07H7B.20, PANC, RV3602C
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: PS, PANTOATE--BETA-ALANINE LIGASE, PANTOATE-ACTIVATING ENZYME

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
10JD2Ligand/Ion(2S)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID
215N2Ligand/Ion(2R)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID
3EDO3Ligand/Ion1,2-ETHANEDIOL
4EOH3Ligand/IonETHANOL
5GOL1Ligand/IonGLYCEROL
Biological Unit 1 (5, 11)
No.NameCountTypeFull Name
10JD2Ligand/Ion(2S)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID
215N2Ligand/Ion(2R)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID
3EDO3Ligand/Ion1,2-ETHANEDIOL
4EOH3Ligand/IonETHANOL
5GOL1Ligand/IonGLYCEROL
Biological Unit 2 (4, 5)
No.NameCountTypeFull Name
10JD1Ligand/Ion(2S)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID
215N1Ligand/Ion(2R)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID
3EDO1Ligand/Ion1,2-ETHANEDIOL
4EOH2Ligand/IonETHANOL
5GOL-1Ligand/IonGLYCEROL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:109 , TYR A:110 , PRO A:111 , ASP A:112 , GLY A:113 , LEU A:114 , ARG A:115 , THR A:116 , LYS A:145 , ASP B:174BINDING SITE FOR RESIDUE GOL A 401
02AC2SOFTWAREPRO A:38 , THR A:39 , MET A:40 , HIS A:47 , VAL A:143 , GLN A:164 , HOH A:558BINDING SITE FOR RESIDUE 0JD A 402
03AC3SOFTWAREPRO A:38 , THR A:39 , MET A:40 , HIS A:47 , VAL A:143 , GLN A:164 , HOH A:558BINDING SITE FOR RESIDUE 15N A 403
04AC4SOFTWAREPRO A:111 , ASP A:112BINDING SITE FOR RESIDUE EDO A 404
05AC5SOFTWARELEU A:114 , ARG A:115 , THR A:117 , GLN B:119 , PRO B:120 , GLY B:121BINDING SITE FOR RESIDUE EDO A 405
06AC6SOFTWAREMET A:71 , TYR A:110BINDING SITE FOR RESIDUE EOH A 406
07AC7SOFTWARESER B:24 , ARG B:25 , ARG B:28 , VAL B:150 , ARG B:151BINDING SITE FOR RESIDUE EOH B 401
08AC8SOFTWAREPRO B:38 , THR B:39 , MET B:40 , HIS B:47 , VAL B:143 , PHE B:157 , GLN B:164BINDING SITE FOR RESIDUE 15N B 402
09AC9SOFTWAREPRO A:133BINDING SITE FOR RESIDUE EOH B 404
10BC1SOFTWAREPRO B:38 , THR B:39 , MET B:40 , HIS B:47 , VAL B:143 , GLN B:164BINDING SITE FOR RESIDUE 0JD B 403
11BC2SOFTWARETYR B:110 , LEU B:114 , GLY B:138BINDING SITE FOR RESIDUE EDO B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G5F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G5F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G5F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G5F)

(-) Exons   (0, 0)

(no "Exon" information available for 4G5F)

(-) 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:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4g5fa_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...eeeeeee..............hhhhhhhhhhhhh..eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeeee..........eeeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g5f A   4 PAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
                                    13        23        33        43        53        63        73|       87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287  
                                                                                                73|                                                                                                                                                                                                                   
                                                                                                 78                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains d4g5fb_ B: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhh..eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....eeeeeeee..........eeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g5f B   2 AIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIG 288
                                    11        21        31        41        51        61        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  
                                                                                               70|                                                                                                                                                                                                          
                                                                                                86
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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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G5F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G5F)

(-) Gene Ontology  (13, 20)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PANC_MYCTO | P9WIL4: 1mop 1n2b 1n2e 1n2g 1n2h 1n2i 1n2j 1n2o 2a7x 2a84 2a86 2a88 3cov 3cow 3coy 3coz 3imc 3ime 3img 3iob 3ioc 3iod 3ioe 3isj 3iub 3iue 3ivc 3ivg 3ivx 3le8 4ddh 4ddk 4ddm 4de5 4ef6 4efk 4fzj 4g5y 4mq6 4mue 4muf 4mug 4muh 4mui 4muj 4muk 4mul 4mun
        PANC_MYCTU | P9WIL5: 1mop 1n2b 1n2e 1n2g 1n2h 1n2i 1n2j 1n2o 2a7x 2a84 2a86 2a88 3cov 3cow 3coy 3coz 3imc 3ime 3img 3iob 3ioc 3iod 3ioe 3isj 3iub 3iue 3ivc 3ivg 3ivx 3le8 4ddh 4ddk 4ddm 4de5 4ef6 4efk 4fzj 4g5y 4mq6 4mue 4muf 4mug 4muh 4mui 4muj 4muk 4mul 4mun

(-) Related Entries Specified in the PDB File

4ddh 4ddk 4ddm 4ef6 4efk 4fzj