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(-) Description

Title :  PHOSPHOPANTOTHENOYLCYSTEINE SYNTHETASE FROM E. COLI, 4'-PHOSPHOPANTOTHENOYL-CMP COMPLEX
 
Authors :  S. Stanitzek, M. A. Augustin, R. Huber, T. Kupke, S. Steinbacher
Date :  04 Aug 04  (Deposition) - 30 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Coenzyme A Biosynthesis, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Stanitzek, M. A. Augustin, R. Huber, T. Kupke, S. Steinbacher
Structural Basis Of Ctp-Dependent Peptide Bond Formation In Coenzyme A Biosynthesis Catalyzed By Escherichia Coli Ppc Synthetase
Structure V. 12 1977 2004
PubMed-ID: 15530362  |  Reference-DOI: 10.1016/J.STR.2004.08.007
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COENZYME A BIOSYNTHESIS BIFUNCTIONAL PROTEIN COABC
    Chains: A, B, C
    EC Number: 6.3.2.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PHOSPHOPANTOTHENOYLCYSTEINE SYNTHETASE(RESIDUES 181-406)
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1PMT3Ligand/IonPHOSPHORIC ACID MONO-[3-(3-{[5-(4-AMINO-2-OXO-2H-PYRIMIDIN-1-YL)-3,4- DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY-PHOSPHORYLOXY}-3-OXO-PROPYLCARBAMOYL)-3-HYDROXY-2,2- DIMETHYL-PROPYL] ESTER
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PMT2Ligand/IonPHOSPHORIC ACID MONO-[3-(3-{[5-(4-AMINO-2-OXO-2H-PYRIMIDIN-1-YL)-3,4- DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY-PHOSPHORYLOXY}-3-OXO-PROPYLCARBAMOYL)-3-HYDROXY-2,2- DIMETHYL-PROPYL] ESTER
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PMT2Ligand/IonPHOSPHORIC ACID MONO-[3-(3-{[5-(4-AMINO-2-OXO-2H-PYRIMIDIN-1-YL)-3,4- DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY-PHOSPHORYLOXY}-3-OXO-PROPYLCARBAMOYL)-3-HYDROXY-2,2- DIMETHYL-PROPYL] ESTER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:212 , SER A:213 , GLY A:214 , LYS A:215 , MET A:216 , GLY A:273 , CYS A:274 , ALA A:275 , ALA A:276 , VAL A:277 , ASP A:279 , PRO A:308 , ASP A:309 , ILE A:310 , VAL A:311 , GLY A:326 , PHE A:327 , ALA A:329 , LYS A:341 , LYS A:345 , ASN A:353 , GLY A:361 , PHE A:362 , ASN A:363 , LYS A:385 , HOH A:507 , HOH A:511 , HOH A:525 , HOH A:555 , LYS B:289BINDING SITE FOR RESIDUE PMT A 500
2AC2SOFTWARELYS A:289 , SER B:212 , SER B:213 , GLY B:214 , LYS B:215 , MET B:216 , GLY B:273 , CYS B:274 , ALA B:275 , ALA B:276 , VAL B:277 , ASP B:279 , PRO B:308 , ASP B:309 , ILE B:310 , VAL B:311 , GLY B:326 , PHE B:327 , ALA B:329 , LYS B:341 , LYS B:345 , ASN B:353 , PHE B:362 , ASN B:363 , LYS B:385 , HOH B:1508 , HOH B:1525 , HOH B:1535 , HOH B:1547 , HOH B:1564 , HOH B:1590BINDING SITE FOR RESIDUE PMT B 1500
3AC3SOFTWARESER C:212 , SER C:213 , GLY C:214 , LYS C:215 , MET C:216 , GLY C:273 , CYS C:274 , ALA C:275 , ALA C:276 , VAL C:277 , ASP C:279 , LYS C:289 , PRO C:308 , ASP C:309 , ILE C:310 , VAL C:311 , GLY C:326 , PHE C:327 , ALA C:329 , LYS C:341 , LYS C:345 , ASN C:353 , PHE C:362 , ASN C:363 , LYS C:385 , HOH C:2504 , HOH C:2506 , HOH C:2537 , HOH C:2572BINDING SITE FOR RESIDUE PMT C 2500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U7Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U7Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U7Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U7Z)

(-) Exons   (0, 0)

(no "Exon" information available for 1U7Z)

(-) 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:216
 aligned with COABC_ECOLI | P0ABQ0 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:223
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402   
          COABC_ECOLI   183 VNDLKHLNIMITAGPTREPLDPVRYISNHSSGKMGFAIAAAAARRGANVTLVSGPVSLPTPPFVKRVDVMTALEMEAAVNASVQQQNIFIGCAAVADYRAATVAPEKIKKQATQGDELTIKMVKNPDIVAGVAALKDHRPYVVGFAAETNNVEEYARQKRIRKNLDLICANDVSQPTQGFNSDNNALHLFWQDGDKVLPLERKELLGQLLLDEIVTRYDEKNR 405
               SCOP domains d1u7za_ A: Coenzyme A biosynthesis bifunctional protein CoaBC, phosphopantothenoylcysteine synthase domain (       CoaB)                                                                                                        SCOP domains
               CATH domains 1u7zA00 A:183-405 Phosphopantothenoylcysteine synthetase. Chain A                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee...eee....eeeee...hhhhhhhhhhhhhh..eeeeee..........eeeee..hhhhhhhhhhhhhhhh.eeee......eee........-------.eeeeeeee..hhhhhhhhh.....eeeeeeee..hhhhhhhhhhhhhh..eeeeee...........eeeeeeee..eeeeeeeeehhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u7z A 183 VNDLKHLNIMITAGPTREPLDPVRYISDHSSGKMGFAIAAAAARRGANVTLVSGPVSLPTPPFVKRVDVMTALEMEAAVNASVQQQNIFIGCAAVADYRAATVAPEKI-------DELTIKMVKNPDIVAGVAALKDHRPYVVGFAAETNNVEEYARQKRIRKNLDLICANDVSQPTQGFNSDNNALHLFWQDGDKVLPLERKELLGQLLLDEIVTRYDEKNR 405
                                   192       202       212       222       232       242       252       262       272       282       | -     | 302       312       322       332       342       352       362       372       382       392       402   
                                                                                                                                     290     298                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with COABC_ECOLI | P0ABQ0 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:226
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400      
          COABC_ECOLI   181 SPVNDLKHLNIMITAGPTREPLDPVRYISNHSSGKMGFAIAAAAARRGANVTLVSGPVSLPTPPFVKRVDVMTALEMEAAVNASVQQQNIFIGCAAVADYRAATVAPEKIKKQATQGDELTIKMVKNPDIVAGVAALKDHRPYVVGFAAETNNVEEYARQKRIRKNLDLICANDVSQPTQGFNSDNNALHLFWQDGDKVLPLERKELLGQLLLDEIVTRYDEKNRR 406
               SCOP domains d1u7zb_ B: Coenzyme A biosynthesis bifunctional protein CoaBC, phosphopantothenoylcysteine synthase domain (Co        aB)                                                                                                          SCOP domains
               CATH domains 1u7zB00 B:181-406 Phosphopantothenoylcysteine synthetase. Chain A                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee...eee....eeeee...hhhhhhhhhhhhh...eeeeee...........eeee..hhhhhhhhhhhhhhhh.eeee......eee........--------.eeeeeee..hhhhhhhh......eeeeeeee..hhhhhhhhhhhhh...eeeeee...........eeeeeeee..eeeeeeeeehhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u7z B 181 SPVNDLKHLNIMITAGPTREPLDPVRYISDHSSGKMGFAIAAAAARRGANVTLVSGPVSLPTPPFVKRVDVMTALEMEAAVNASVQQQNIFIGCAAVADYRAATVAPEKI--------ELTIKMVKNPDIVAGVAALKDHRPYVVGFAAETNNVEEYARQKRIRKNLDLICANDVSQPTQGFNSDNNALHLFWQDGDKVLPLERKELLGQLLLDEIVTRYDEKNRR 406
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400      
                                                                                                                                       290      299                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:219
 aligned with COABC_ECOLI | P0ABQ0 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:225
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400     
          COABC_ECOLI   181 SPVNDLKHLNIMITAGPTREPLDPVRYISNHSSGKMGFAIAAAAARRGANVTLVSGPVSLPTPPFVKRVDVMTALEMEAAVNASVQQQNIFIGCAAVADYRAATVAPEKIKKQATQGDELTIKMVKNPDIVAGVAALKDHRPYVVGFAAETNNVEEYARQKRIRKNLDLICANDVSQPTQGFNSDNNALHLFWQDGDKVLPLERKELLGQLLLDEIVTRYDEKNR 405
               SCOP domains d1u7zc_ C: Coenzyme A biosynthesis bifunctional protein CoaBC, phosphopantothenoylcysteine synthase domain (CoaB      )                                                                                                           SCOP domains
               CATH domains 1u7zC00 C:181-405 Phosphopantothenoylcysteine synthetase. Chain A                                                                                                                                                                 CATH domains
           Pfam domains (1) -----DFP-1u7zC01 C:186-372                                                                                                                                                                      --------------------------------- Pfam domains (1)
           Pfam domains (2) -----DFP-1u7zC02 C:186-372                                                                                                                                                                      --------------------------------- Pfam domains (2)
           Pfam domains (3) -----DFP-1u7zC03 C:186-372                                                                                                                                                                      --------------------------------- Pfam domains (3)
         Sec.struct. author .........eeeeee...eee.....eee....hhhhhhhhhhhhhh..eeeeee...........eeee..hhhhhhhhhhhhhhhh.eeee......eee..........------.....eee..hhhhhhhh......eeeeeeee..hhhhhhhhhhhhhh..eeeeee...........eeeeeeee..eeeeeeeeehhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u7z C 181 SPVNDLKHLNIMITAGPTREPLDPVRYISDHSSGKMGFAIAAAAARRGANVTLVSGPVSLPTPPFVKRVDVMTALEMEAAVNASVQQQNIFIGCAAVADYRAATVAPEKIKK------ELTIKMVKNPDIVAGVAALKDHRPYVVGFAAETNNVEEYARQKRIRKNLDLICANDVSQPTQGFNSDNNALHLFWQDGDKVLPLERKELLGQLLLDEIVTRYDEKNR 405
                                   190       200       210       220       230       240       250       260       270       280       290 |     300       310       320       330       340       350       360       370       380       390       400     
                                                                                                                                         292    299
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Family: DFP (5)
(-)
Escherichia coli (strain K12) (4)
1aDFP-1u7zC01C:186-372
1bDFP-1u7zC02C:186-372
1cDFP-1u7zC03C:186-372

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (COABC_ECOLI | P0ABQ0)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004632    phosphopantothenate--cysteine ligase activity    Catalysis of the reaction: CTP + (R)-4'-phosphopantothenate + L-cysteine = CMP + diphosphate + (R)-4'-phosphopantothenoyl-L-cysteine. Cysteine can be replaced by some of its derivatives.
    GO:0004633    phosphopantothenoylcysteine decarboxylase activity    Catalysis of the reaction: N-[(R)-4-phosphonatopantothenoyl]-L-cysteinate + H(+) = CO(2) + pantetheine 4'-phosphate.
biological process
    GO:0015937    coenzyme A biosynthetic process    The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0015941    pantothenate catabolic process    The chemical reactions and pathways resulting in the breakdown 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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        COABC_ECOLI | P0ABQ0: 1u7u 1u7w 1u80

(-) Related Entries Specified in the PDB File

1u7u THE SAME PROTEIN, APO
1u7w THE SAME PROTEIN, CTP-COMPLEX
1u80 THE SAME PROTEIN, CMP COMPLEX