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(-) Description

Title :  CRYSTAL STRUCTURE OF PKM2-K422R MUTANT
 
Authors :  P. Wang, C. Sun, T. Zhu, Y. Xu
Date :  22 May 14  (Deposition) - 25 Feb 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tetramer, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Wang, C. Sun, T. Zhu, Y. Xu
Structural Insight Into Mechanisms For Dynamic Regulation O Pkm2
Protein Cell 2015
PubMed-ID: 25645022  |  Reference-DOI: 10.1007/S13238-015-0132-X

(-) Compounds

Molecule 1 - PYRUVATE KINASE PKM
    Chains: A, B, C, D
    EC Number: 2.7.1.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PKM, OIP3, PK2, PK3, PKM2
    Mutation: YES
    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  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2K4Ligand/IonPOTASSIUM ION
3SO49Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:75 , SER A:77 , ASP A:113 , THR A:114 , HOH A:1102 , HOH A:1132BINDING SITE FOR RESIDUE K A 1001
02AC2SOFTWARELYS A:433 , TRP A:482 , ARG A:489BINDING SITE FOR RESIDUE SO4 A 1002
03AC3SOFTWARETHR A:432 , LYS A:433 , SER A:434 , GLY A:435 , ARG A:436 , SER A:437 , THR A:522 , HOH A:1142BINDING SITE FOR RESIDUE SO4 A 1003
04AC4SOFTWAREASN A:75 , HIS A:78 , ARG A:120 , HOH A:1132 , HOH A:1169 , HOH A:1223BINDING SITE FOR RESIDUE SO4 A 1004
05AC5SOFTWAREARG A:43 , ASN A:44 , ASN A:70 , ARG A:106 , HIS A:464 , PHE A:470 , HOH A:1225 , HOH A:1237 , HOH A:1241BINDING SITE FOR RESIDUE GOL A 1005
06AC6SOFTWAREASN B:75 , SER B:77 , ASP B:113 , THR B:114BINDING SITE FOR RESIDUE K B 1001
07AC7SOFTWARETHR B:432 , LYS B:433 , SER B:434 , GLY B:435 , ARG B:436 , SER B:437BINDING SITE FOR RESIDUE SO4 B 1002
08AC8SOFTWARELYS B:433 , TRP B:482 , ARG B:489 , HOH B:1153BINDING SITE FOR RESIDUE SO4 B 1003
09AC9SOFTWAREARG B:43 , ASN B:44 , ASN B:70 , HIS B:464 , TYR B:466 , ILE B:469 , PRO B:471BINDING SITE FOR RESIDUE GOL B 1004
10BC1SOFTWAREASN C:75 , SER C:77 , ASP C:113 , THR C:114 , HOH C:1101BINDING SITE FOR RESIDUE K C 1001
11BC2SOFTWARETHR C:432 , LYS C:433 , SER C:434 , ARG C:436 , SER C:437 , HOH C:1180BINDING SITE FOR RESIDUE SO4 C 1002
12BC3SOFTWARETRP C:482 , ARG C:489 , GLY C:518BINDING SITE FOR RESIDUE SO4 C 1003
13BC4SOFTWAREARG C:43 , HIS C:464 , ILE C:469BINDING SITE FOR RESIDUE GOL C 1004
14BC5SOFTWAREASN D:75 , SER D:77 , ASP D:113 , THR D:114 , HOH D:1107BINDING SITE FOR RESIDUE K D 1001
15BC6SOFTWARELYS D:433 , TRP D:482 , ARG D:489BINDING SITE FOR RESIDUE SO4 D 1002
16BC7SOFTWARETHR D:432 , LYS D:433 , SER D:434 , ARG D:436 , SER D:437 , HOH D:1128BINDING SITE FOR RESIDUE SO4 D 1003
17BC8SOFTWAREARG D:43 , ASN D:44 , ASN D:70 , ARG D:106 , HIS D:464 , ILE D:469 , PHE D:470 , HOH D:1102 , HOH D:1169BINDING SITE FOR RESIDUE GOL D 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:121 -Gly A:122
2Pro D:212 -Gly D:213

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QGC)

(-) 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:503
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.............eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh...........eeeee................eee....eeeee.hhhhh......eee....hhhhh.....eeee....eeeeeeee...eeeeeeee.eee.....ee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeee..........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qgc A  24 DTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPDPTEATAVGAVEASFRCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    33        43        53        63        73        83        93       103       113       123  ||   135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       408       418       428       438       448       458       468       478       488       498       508       518       528   
                                                                                                                                126|                                                                                                                                                                                                                                                                               403|                                                                                                                            
                                                                                                                                 129                                                                                                                                                                                                                                                                                407                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:499
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.............eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh...........eeeee.....ee.................eee............eee..............eeee....eeee............eee........eee.......hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeee..........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qgc B  24 DTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPSDPTEATAVGAVEASFRCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    33        43        53        63        73        83        93       103       113       123  ||   136       146       156       166       176       186       196       206     ||220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400  ||   412       422       432       442       452       462       472       482       492       502       512       522         
                                                                                                                                126|                                                                               212|                                                                                                                                                                                       403|                                                                                                                             
                                                                                                                                 130                                                                                217                                                                                                                                                                                        406                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh.............eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh...........eeeee.....ee........eee...eeeeee.hhhhh......eee..hhhhhh......eeee....eeeeeeee...eeeeeeee.eee....eee.......hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhh...eeeeehhhhhhhh...hhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeee..........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qgc C  24 DTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLTSDPTEATAVGAVEASFRCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    33        43        53        63        73        83        93       103       113       123  ||   136       146       156       166       176       186       196       206     ||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|                                                                               212|                                                                                                                                                                                     401|                                                                                                                              
                                                                                                                                 130                                                                                217                                                                                                                                                                                      405                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:500
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.............eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh...........eeeee......................eeee....................hhhhh.....eeee....eeeeeeee....eeeeeee.........ee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeee..........eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qgc D  25 TFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLSDPTEATAVGAVEASFRCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    34        44        54        64        74        84        94       104       114       124 ||    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   ||  411       421       431       441       451       461       471       481       491       501       511       521       531
                                                                                                                               126|                                                                                                                                                                                                                                                                            401|                                                                                                                             
                                                                                                                                130                                                                                                                                                                                                                                                                             406
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4QGC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)

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  KPYM_HUMAN | P14618
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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 4fxj 4g1n 4jpg 4qg6 4qg8 4qg9 4rpp 4wj8 4yj5 5x1v 5x1w

(-) Related Entries Specified in the PDB File

4qg6 4qg8 4qg9 4rpp