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(-) Description

Title :  CRYSTAL STRUCTURE OF TON1374 IN COMPLEX WITH ATP
 
Authors :  M. -K. Kim, Y. J. An, S. -S. Cha
Date :  19 Aug 13  (Deposition) - 06 Aug 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ligase, Atp Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. -K. Kim, Y. J. An, S. -S. Cha
The Crystal Structure Of A Novel Phosphopantothenate Synthetase From The Hyperthermophilic Archaea, Thermococcus Onnurineus Na1
Biochem. Biophys. Res. Commun. V. 439 533 2013
PubMed-ID: 24021277  |  Reference-DOI: 10.1016/J.BBRC.2013.09.008

(-) Compounds

Molecule 1 - PHOSPHOPANTOTHENATE SYNTHETASE
    Chains: A, B, C, D
    EC Number: 6.3.2.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TON_1374
    Organism Scientific: THERMOCOCCUS ONNURINEUS
    Organism Taxid: 523850
    Strain: NA1
    Synonym: PUTATIVE UNCHARACTERIZED PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1ATP4Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:36 , ARG A:39 , GLY A:40 , LEU A:161 , ASP A:163 , ASP A:181 , LEU A:182 , ASN A:183 , ASP A:198 , ASN A:199 , ILE A:200 , MG A:302 , HOH A:404 , HOH A:405 , ARG B:17BINDING SITE FOR RESIDUE ATP A 301
2AC2SOFTWAREATP A:301BINDING SITE FOR RESIDUE MG A 302
3AC3SOFTWAREARG A:17 , TYR A:45 , ALA B:36 , ARG B:39 , LEU B:161 , GLU B:162 , ASP B:163 , GLY B:164 , ASP B:181 , LEU B:182 , ARG B:187 , SER B:188 , ASP B:198 , ASN B:199 , ILE B:200 , HOH B:425BINDING SITE FOR RESIDUE ATP B 301
4AC4SOFTWAREALA C:36 , ARG C:39 , GLY C:40 , LEU C:161 , ASP C:181 , LEU C:182 , ASP C:198 , ASN C:199 , ILE C:200 , HOH C:419 , ARG D:10 , ARG D:17BINDING SITE FOR RESIDUE ATP C 301
5AC5SOFTWAREARG C:17 , TYR C:45 , ALA D:36 , ARG D:39 , LEU D:161 , GLU D:162 , ASP D:163 , ASP D:181 , LEU D:182 , ASN D:183 , SER D:186 , ASP D:198 , ASN D:199 , ILE D:200BINDING SITE FOR RESIDUE ATP D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MB2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg B:256 -Lys B:257
2His D:141 -Glu D:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MB2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MB2)

(-) Exons   (0, 0)

(no "Exon" information available for 4MB2)

(-) 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:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhh....ee.....ee.........ee...hhhhh.eee....hhhhhhhhhhh..eeeee.....hhhhhhh.eee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mb2 A   9 PRYWSLYYREKIIEGMEKGMTAKAGLIAHGRGEAFDYLIGERTIEPAERAMRAAVAKLLLAENPVVSVNGNVAALVPKETIELARALNAKLEINLFYRTEDRVKAIAEELRKYDPEIELLGINPTKRIPGLEHERGKVDENGIWKADVVVVPLEDGDRTEALVRMGKFVITIDLNPLSRSARMADITIVDNIVRAYPRMTELAREMKDYSRGELIRIIEEYDNGKTLNDVLLHIRDRLTKLAEGGIWRKKQL 260
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  


Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh......ee...........................eee....hhhhhhhhhhhh.eeeee.....hhhhhhh.eee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mb2 B   2 VKIPKSHPRYWSLYYREKIIEGMEKGMTAKAGLIAHGRGEAFDYLIGERTIEPAERAMRAAVAKLLLAENPVVSVNGNVAALVPKETIELARALNAKLEINLFYRTEDRVKAIAEELRKYDPEIELLGINPTKRIPGLEHERGKVDENGIWKADVVVVPLEDGDRTEALVRMGKFVITIDLNPLSRSARMADITIVDNIVRAYPRMTELAREMKDYSRGELIRIIEEYDNGKTLNDVLLHIRDRLTKLAEGGIWRKK 258
                                    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       


Chain C from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh......ee.....ee....ee.........eee....hhhhhhhhhhhh.eeeee.....hhhhhhh.eee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mb2 C   9 PRYWSLYYREKIIEGMEKGMTAKAGLIAHGRGEAFDYLIGERTIEPAERAMRAAVAKLLLAENPVVSVNGNVAALVPKETIELARALNAKLEINLFYRTEDRVKAIAEELRKYDPEIELLGINPTKRIPGGKVDENGIWKADVVVVPLEDGDRTEALVRMGKFVITIDLNPLSRSARMADITIVDNIVRAYPRMTELAREMKDYSRGELIRIIEEYDNGKTLNDVLLHIRDRLTKLAEGGIWRKKQ 259
                                    18        28        38        48        58        68        78        88        98       108       118       128       138|      153       163       173       183       193       203       213       223       233       243       253      
                                                                                                                                                           138|                                                                                                                   
                                                                                                                                                            144                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh....ee.....ee........ee.........eee....hhhhhhhhhhhh.eeeee.....hhhhhhh.eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mb2 D   7 SHPRYWSLYYREKIIEGMEKGMTAKAGLIAHGRGEAFDYLIGERTIEPAERAMRAAVAKLLLAENPVVSVNGNVAALVPKETIELARALNAKLEINLFYRTEDRVKAIAEELRKYDPEIELLGINPTKRIPGLEHEGKVDENGIWKADVVVVPLEDGDRTEALVRMGKFVITIDLNPLSRSARMADITIVDNIVRAYPRMTELAREMKDYSRGELIRIIEEYDNGKTLNDVLLHIRDRLTKLAEGGIWRKKQLD 261
                                    16        26        36        46        56        66        76        86        96       106       116       126       136     ||147       157       167       177       187       197       207       217       227       237       247       257    
                                                                                                                                                                 142|                                                                                                                     
                                                                                                                                                                  144
   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 4MB2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MB2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MB2)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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4mb0