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(-) Description

Title :  STRUCTURAL BASIS FOR THE FEEDBACK REGULATION OF ESCHERICHIA COLI PANTOTHENATE KINASE BY COENZYME A
 
Authors :  M. Yun, C. G. Park, J. Y. Kim, C. O. Rock, S. Jackowski, H. W. Park
Date :  10 Apr 00  (Deposition) - 17 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Crystal Structure, Protein-Inhibitor Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Yun, C. G. Park, J. Y. Kim, C. O. Rock, S. Jackowski, H. W. Park
Structural Basis For The Feedback Regulation Of Escherichia Coli Pantothenate Kinase By Coenzyme A.
J. Biol. Chem. V. 275 28093 2000
PubMed-ID: 10862768
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PANTOTHENATE KINASE
    ChainsA, B, C, D
    EC Number2.7.1.33
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET21
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymPANK

 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  (3, 32)

Asymmetric Unit (3, 32)
No.NameCountTypeFull Name
1ANP4Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG4Ligand/IonMAGNESIUM ION
3MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:102 , GLU A:199 , ANP A:401BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWARESER B:102 , GLU B:199 , ANP B:402BINDING SITE FOR RESIDUE MG B 502
3AC3SOFTWARESER C:102 , GLU C:199 , ANP C:403BINDING SITE FOR RESIDUE MG C 503
4AC4SOFTWARESER D:102 , GLU D:199 , ANP D:404BINDING SITE FOR RESIDUE MG D 504
5AC5SOFTWAREASN A:43 , ASP A:45 , LEU A:46 , TYR A:55 , VAL A:97 , ALA A:98 , VAL A:99 , GLY A:100 , LYS A:101 , SER A:102 , THR A:103 , GLU A:199 , ARG A:243 , LYS A:303 , HIS A:307 , MG A:501 , HOH A:5136BINDING SITE FOR RESIDUE ANP A 401
6AC6SOFTWAREASN B:43 , ASP B:45 , TYR B:55 , VAL B:97 , ALA B:98 , VAL B:99 , GLY B:100 , LYS B:101 , SER B:102 , THR B:103 , GLU B:199 , ARG B:243 , LYS B:303 , HIS B:307 , MG B:502 , HOH B:5077 , HOH B:5104 , HOH B:5209BINDING SITE FOR RESIDUE ANP B 402
7AC7SOFTWAREASN C:43 , ASP C:45 , VAL C:97 , ALA C:98 , VAL C:99 , GLY C:100 , LYS C:101 , SER C:102 , THR C:103 , GLU C:199 , ARG C:243 , LYS C:303 , HIS C:307 , MG C:503 , HOH C:5064 , HOH C:5221 , HOH C:5263BINDING SITE FOR RESIDUE ANP C 403
8AC8SOFTWAREASN D:43 , ASP D:45 , TYR D:55 , VAL D:97 , ALA D:98 , VAL D:99 , GLY D:100 , LYS D:101 , SER D:102 , THR D:103 , ARG D:243 , LYS D:303 , HIS D:307 , MG D:504 , HOH D:5110 , HOH D:5306BINDING SITE FOR RESIDUE ANP D 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ESN)

(-) 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:311
 aligned with COAA_ECOLI | P0A6I3 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:311
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315 
           COAA_ECOLI     6 QTLMTPYLQFDRNQWAALRDSVPMTLSEDEIARLKGINEDLSLEEVAEIYLPLSRLLNFYISSNLRRQAVLEQFLGTNGQRIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFLHPNQVLKERGLMKKKGFPESYDMHRLVKFVSDLKSGVPNVTAPVYSHLIYDVIPDGDKTVVQPDILILEGLNVLQSGMDYPHDPHHVFVSDFVDFSIYVDAPEDLLQTWYINRFLKFREGAFTDPDSYFHNYAKLTKEEAIKTAMTLWKEINWLNLKQNILPTRERASLILTKSANHAVEEVRLRK 316
               SCOP domains d1esna_ A: Pantothenate kinase PanK                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1esnA00 A:6-316 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeehhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee....hhhhhhhhhhhhhhh......eeeee.hhh..hhhhhhhh.......hhhh.hhhhhhhhhhhhh....eeee..ee....ee.....eeee...eeeee......hhhhh.......hhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhh.......hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1esn A   6 QTLmTPYLQFDRNQWAALRDSVPmTLSEDEIARLKGINEDLSLEEVAEIYLPLSRLLNFYISSNLRRQAVLEQFLGTNGQRIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFLHPNQVLKERGLmKKKGFPESYDmHRLVKFVSDLKSGVPNVTAPVYSHLIYDVIPDGDKTVVQPDILILEGLNVLQSGmDYPHDPHHVFVSDFVDFSIYVDAPEDLLQTWYINRFLKFREGAFTDPDSYFHNYAKLTKEEAIKTAmTLWKEINWLNLKQNILPTRERASLILTKSANHAVEEVRLRK 316
                               |    15        25   |    35        45        55        65        75        85        95       105       115       125       135      |145       155       165       175       185       195       205  |    215       225       235       245       255       265       275       285       295       305       315 
                               |                  29-MSE                                                                                                          142-MSE    153-MSE                                                208-MSE                                                            275-MSE                                     
                               9-MSE                                                                                                                                                                                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with COAA_ECOLI | P0A6I3 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:309
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307         
           COAA_ECOLI     8 LMTPYLQFDRNQWAALRDSVPMTLSEDEIARLKGINEDLSLEEVAEIYLPLSRLLNFYISSNLRRQAVLEQFLGTNGQRIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFLHPNQVLKERGLMKKKGFPESYDMHRLVKFVSDLKSGVPNVTAPVYSHLIYDVIPDGDKTVVQPDILILEGLNVLQSGMDYPHDPHHVFVSDFVDFSIYVDAPEDLLQTWYINRFLKFREGAFTDPDSYFHNYAKLTKEEAIKTAMTLWKEINWLNLKQNILPTRERASLILTKSANHAVEEVRLRK 316
               SCOP domains d1esnb_ B: Pantothenate kinase PanK                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1esnB00 B:8-316 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhh..........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhh.......eeeee.hhh..hhhhhhhh.......hhhh.hhhhhhhhhhhhh....eeee..ee....ee.....eeee...eeeee......hhhhh.......hhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1esn B   8 LmTPYLQFDRNQWAALRDSVPmTLSEDEIARLKGINEDLSLEEVAEIYLPLSRLLNFYISSNLRRQAVLEQFLGTNGQRIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFLHPNQVLKERGLmKKKGFPESYDmHRLVKFVSDLKSGVPNVTAPVYSHLIYDVIPDGDKTVVQPDILILEGLNVLQSGmDYPHDPHHVFVSDFVDFSIYVDAPEDLLQTWYINRFLKFREGAFTDPDSYFHNYAKLTKEEAIKTAmTLWKEINWLNLKQNILPTRERASLILTKSANHAVEEVRLRK 316
                             |      17        27 |      37        47        57        67        77        87        97       107       117       127       137    |  147     | 157       167       177       187       197       207|      217       227       237       247       257       267       277       287       297       307         
                             9-MSE              29-MSE                                                                                                          142-MSE    153-MSE                                                208-MSE                                                            275-MSE                                     

Chain C from PDB  Type:PROTEIN  Length:309
 aligned with COAA_ECOLI | P0A6I3 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:309
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307         
           COAA_ECOLI     8 LMTPYLQFDRNQWAALRDSVPMTLSEDEIARLKGINEDLSLEEVAEIYLPLSRLLNFYISSNLRRQAVLEQFLGTNGQRIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFLHPNQVLKERGLMKKKGFPESYDMHRLVKFVSDLKSGVPNVTAPVYSHLIYDVIPDGDKTVVQPDILILEGLNVLQSGMDYPHDPHHVFVSDFVDFSIYVDAPEDLLQTWYINRFLKFREGAFTDPDSYFHNYAKLTKEEAIKTAMTLWKEINWLNLKQNILPTRERASLILTKSANHAVEEVRLRK 316
               SCOP domains d1esnc_ C: Pantothenate kinase PanK                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1esnC00 C:8-316 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhh.............hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhh.......eeeee.hhh..hhhhhhhh.......hhhh.hhhhhhhhhhhhh....eeee..ee....ee.....eeee...eeeee......hhhhh.......hhhhhh.eeeeee.hhhhhhhhhhhhhhhhh..........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1esn C   8 LmTPYLQFDRNQWAALRDSVPmTLSEDEIARLKGINEDLSLEEVAEIYLPLSRLLNFYISSNLRRQAVLEQFLGTNGQRIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFLHPNQVLKERGLmKKKGFPESYDmHRLVKFVSDLKSGVPNVTAPVYSHLIYDVIPDGDKTVVQPDILILEGLNVLQSGmDYPHDPHHVFVSDFVDFSIYVDAPEDLLQTWYINRFLKFREGAFTDPDSYFHNYAKLTKEEAIKTAmTLWKEINWLNLKQNILPTRERASLILTKSANHAVEEVRLRK 316
                             |      17        27 |      37        47        57        67        77        87        97       107       117       127       137    |  147     | 157       167       177       187       197       207|      217       227       237       247       257       267       277       287       297       307         
                             9-MSE              29-MSE                                                                                                          142-MSE    153-MSE                                                208-MSE                                                            275-MSE                                     

Chain D from PDB  Type:PROTEIN  Length:309
 aligned with COAA_ECOLI | P0A6I3 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:309
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307         
           COAA_ECOLI     8 LMTPYLQFDRNQWAALRDSVPMTLSEDEIARLKGINEDLSLEEVAEIYLPLSRLLNFYISSNLRRQAVLEQFLGTNGQRIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFLHPNQVLKERGLMKKKGFPESYDMHRLVKFVSDLKSGVPNVTAPVYSHLIYDVIPDGDKTVVQPDILILEGLNVLQSGMDYPHDPHHVFVSDFVDFSIYVDAPEDLLQTWYINRFLKFREGAFTDPDSYFHNYAKLTKEEAIKTAMTLWKEINWLNLKQNILPTRERASLILTKSANHAVEEVRLRK 316
               SCOP domains d1esnd_ D: Pantothenate kinase PanK                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1esnD00 D:8-316 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhh..........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhh.......eeeee.hhh..hhhhhhhh.......hhhh.hhhhhhhhhhhhh....eeee..ee....ee.....eeee...eeeee......hhhhh.......hhhhhh.eeeeee.hhhhhhhhhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1esn D   8 LmTPYLQFDRNQWAALRDSVPmTLSEDEIARLKGINEDLSLEEVAEIYLPLSRLLNFYISSNLRRQAVLEQFLGTNGQRIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFLHPNQVLKERGLmKKKGFPESYDmHRLVKFVSDLKSGVPNVTAPVYSHLIYDVIPDGDKTVVQPDILILEGLNVLQSGmDYPHDPHHVFVSDFVDFSIYVDAPEDLLQTWYINRFLKFREGAFTDPDSYFHNYAKLTKEEAIKTAmTLWKEINWLNLKQNILPTRERASLILTKSANHAVEEVRLRK 316
                             |      17        27 |      37        47        57        67        77        87        97       107       117       127       137    |  147     | 157       167       177       187       197       207|      217       227       237       247       257       267       277       287       297       307         
                             9-MSE              29-MSE                                                                                                          142-MSE    153-MSE                                                208-MSE                                                            275-MSE                                     

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ESN)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (COAA_ECOLI | P0A6I3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0004594    pantothenate kinase activity    Catalysis of the reaction: ATP + pantothenate = ADP + D-4'-phosphopantothenate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0004849    uridine kinase activity    Catalysis of the reaction: ATP + uridine = ADP + UMP.
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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006206    pyrimidine nucleobase metabolic process    The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
    GO:0043097    pyrimidine nucleoside salvage    Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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)

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        COAA_ECOLI | P0A6I31esm 1sq5

(-) Related Entries Specified in the PDB File

1esm