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(-) Description

Title :  STRUCTURE OF M2 PYRUVATE KINASE IN COMPLEX WITH PHENYLALANINE
 
Authors :  M. D. Walkinshaw, H. P. Morgan
Date :  03 Jul 12  (Deposition) - 27 Mar 13  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim Barrel, Transferase, Phenylalanine Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. Morgan, F. J. O'Reilly, M. A. Wear, J. R. O'Neill, L. A. Fothergill-Gilmore, T. Hupp, M. D. Walkinshaw
M2 Pyruvate Kinase Provides A Mechanism For Nutrient Sensin And Regulation Of Cell Proliferation.
Proc. Natl. Acad. Sci. Usa V. 110 5881 2013
PubMed-ID: 23530218  |  Reference-DOI: 10.1073/PNAS.1217157110

(-) Compounds

Molecule 1 - PYRUVATE KINASE ISOZYMES M1/M2
    Chains: A, B, C, D
    EC Number: 2.7.1.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A_M2
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PET
    Gene: OIP3, PK2, PK3, PKM, PKM2, PYRUVATE KINASE M2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYTOSOLIC THYROID HORMONE-BINDING PROTEIN, CTHBP, OPA- INTERACTING PROTEIN 3, OIP-3, PYRUVATE KINASE 2/3, PYRUVATE KINASE MUSCLE ISOZYME, THYROID HORMONE-BINDING PROTEIN 1, THBP1, TUMOR M2- PK, P58

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1PHE4Mod. Amino AcidPHENYLALANINE
2PO45Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:432 , LYS A:433 , SER A:434 , GLY A:435 , ARG A:436 , SER A:437 , THR A:522BINDING SITE FOR RESIDUE PO4 A 601
2AC2SOFTWAREASN A:75 , HIS A:78 , ARG A:120BINDING SITE FOR RESIDUE PO4 A 602
3AC3SOFTWAREARG A:43 , ASN A:44 , THR A:45 , ASN A:70 , ARG A:106 , HIS A:464 , GLY A:468 , ILE A:469 , PHE A:470 , PRO A:471BINDING SITE FOR RESIDUE PHE A 603
4AC4SOFTWARETHR B:432 , LYS B:433 , SER B:434 , ARG B:436 , SER B:437 , THR B:522 , HOH B:709BINDING SITE FOR RESIDUE PO4 B 601
5AC5SOFTWAREARG B:43 , ASN B:44 , THR B:45 , ASN B:70 , ARG B:106 , HIS B:464 , GLY B:468 , ILE B:469 , PHE B:470BINDING SITE FOR RESIDUE PHE B 602
6AC6SOFTWARETHR C:432 , LYS C:433 , SER C:434 , GLY C:435 , ARG C:436 , SER C:437 , THR C:522BINDING SITE FOR RESIDUE PO4 C 601
7AC7SOFTWAREARG C:43 , ASN C:44 , ASN C:70 , ARG C:106 , HIS C:464 , GLY C:468 , ILE C:469 , PHE C:470BINDING SITE FOR RESIDUE PHE C 602
8AC8SOFTWARETHR D:432 , LYS D:433 , SER D:434 , ARG D:436 , SER D:437 , HOH D:724BINDING SITE FOR RESIDUE PO4 D 601
9AC9SOFTWAREARG D:43 , ASN D:44 , ASN D:70 , ARG D:106 , HIS D:464 , GLY D:468 , ILE D:469 , PHE D:470 , HOH D:722BINDING SITE FOR RESIDUE PHE D 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr B:405 -Ser B:406

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FXJ)

(-) 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:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh............eeeee...............eee....eeeee.hhhhh......eee....hhhhhh....eeee....eeeeeeee...eeeeeeee.eee.....ee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhh...hhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhh.....eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeee..........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fxj A  28 EHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQNLIAREAEAAIYHLQLFEELRRLAPDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    37        47        57        67        77        87        97       107       117       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400  ||   413       423       433       443       453       463       473       483       493       503       513       523        
                                                                                                                            126|                                                                                                                                                                                                                                                                              403|                                                                                                                            
                                                                                                                             130                                                                                                                                                                                                                                                                               407                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.............eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh............eeeee............hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....eeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhhh......eeeeee..........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fxj B  23 ADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQNLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    32        42        52        62        72        82        92       102       112      |218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528   
                                                                                                                          119|                                                                                                                                                                                                                                                                                                                           
                                                                                                                           216                                                                                                                                                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:504
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh.............eeeee......hhhhhhhhhhhheeeeeee....hhhhhhhhhhhhhhhhhhhh.........eeeee..............eee....eeeee.hhhhh......eee..............eeee....eeeeeeee...eeeeeeee.eee.....ee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....eeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeee..........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fxj C  24 DTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQNLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    33        43        53        63        73        83        93       103       113       123  ||   137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527    
                                                                                                                                126|                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                 131                                                                                                                                                                                                                                                                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:508
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.............eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhh.........eeeee.....ee...........eee....eeeee.hhhhh......eee..............eeee....eeeeeeee...eeeeee...eee....eee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeee..........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fxj D  24 DTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQNLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523
   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 4FXJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        KPYM_HUMAN | P14618: 1t5a 1zjh 3bjf 3bjt 3g2g 3gqy 3gr4 3h6o 3me3 3srd 3srf 3srh 3u2z 4b2d 4fxf 4g1n 4jpg 4qg6 4qg8 4qg9 4qgc 4rpp 4wj8 4yj5 5x1v 5x1w

(-) Related Entries Specified in the PDB File

1bjf SAME PROTEIN COMPLEXED WITHOUT ATP
4fxf