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(-) Description

Title :  THE STRUCTURE OF THE YEAST SR PROTEIN KINASE, SKY1P, WITH BOUND ADP
 
Authors :  B. Nolen, J. Ngo, S. Chakrabarti, D. Vu, J. A. Adams, G. Ghosh
Date :  22 Aug 03  (Deposition) - 23 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Nolen, J. Ngo, S. Chakrabarti, D. Vu, J. A. Adams, G. Ghosh
Nucleotide-Induced Conformational Changes In The Saccharomyces Cerevisiae Sr Protein Kinase, Sky1P, Revealed By X-Ray Crystallography
Biochemistry V. 42 9575 2003
PubMed-ID: 12911299  |  Reference-DOI: 10.1021/BI0344331
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SR PROTEIN KINASE
    ChainsA, B
    EC Number2.7.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)PLYS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSKY1PDELTAN(137)DELTAS
    GeneSKY1
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4SO48Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ADE-1Ligand/IonADENINE
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE
2ADP-1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4SO45Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:153 , LYS A:154 , ASP A:155 , PHE A:232 , ASN A:233 , HIS A:234 , LYS A:235 , HOH A:814 , HOH A:843 , HOH A:844 , HOH A:899BINDING SITE FOR RESIDUE SO4 A 801
02AC2SOFTWARETYR B:153 , LYS B:154 , ASP B:155 , PHE B:232 , HIS B:234 , LYS B:235 , HOH B:906 , HOH B:944BINDING SITE FOR RESIDUE SO4 B 802
03AC3SOFTWARESER B:631 , ARG B:635 , ARG B:692 , HOH B:1002 , HOH B:1032BINDING SITE FOR RESIDUE SO4 B 803
04AC4SOFTWAREARG B:568 , ARG B:571 , HOH B:961BINDING SITE FOR RESIDUE SO4 B 804
05AC5SOFTWARESER A:631 , ARG A:635 , ARG A:692 , HOH A:924BINDING SITE FOR RESIDUE SO4 A 805
06AC6SOFTWAREARG A:571 , HOH A:835BINDING SITE FOR RESIDUE SO4 A 806
07AC7SOFTWAREGLY B:609 , HIS B:610 , SER B:611BINDING SITE FOR RESIDUE SO4 B 807
08AC8SOFTWAREARG B:641 , ASN B:645 , SER B:646 , ARG B:651BINDING SITE FOR RESIDUE SO4 B 808
09AC9SOFTWAREASN A:299 , ASP A:550 , ADP A:810BINDING SITE FOR RESIDUE MG A 809
10BC1SOFTWAREGLY A:165 , TRP A:166 , GLY A:167 , HIS A:168 , PHE A:169 , SER A:170 , VAL A:172 , ALA A:185 , LYS A:187 , LEU A:226 , GLU A:247 , LEU A:249 , GLY A:250 , ASN A:252 , GLU A:298 , ASN A:299 , LEU A:301 , ASP A:550 , MG A:809 , HOH A:842BINDING SITE FOR RESIDUE ADP A 810
11BC2SOFTWAREALA B:185 , LEU B:226 , GLU B:247 , VAL B:248 , LEU B:249BINDING SITE FOR RESIDUE ADE B 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q8Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q8Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q8Y)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SKY1_YEAST164-187
 
  2A:164-187
B:164-187
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SKY1_YEAST290-302
 
  2A:290-302
B:290-302
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SKY1_YEAST164-187
 
  1A:164-187
-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SKY1_YEAST290-302
 
  1A:290-302
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SKY1_YEAST164-187
 
  1-
B:164-187
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SKY1_YEAST290-302
 
  1-
B:290-302

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YMR216C1YMR216C.1XIII:701038-6988102229SKY1_YEAST1-7427422A:144-737 (gaps)
B:146-737 (gaps)
594
592

(-) 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:351
 aligned with SKY1_YEAST | Q03656 from UniProtKB/Swiss-Prot  Length:742

    Alignment length:594
                                   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       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733    
           SKY1_YEAST   144 YHPAFKGEPYKDARYILVRKLGWGHFSTVWLAKDMVNNTHVAMKIVRGDKVYTEAAEDEIKLLQRVNDADNTKEDSMGANHILKLLDHFNHKGPNGVHVVMVFEVLGENLLALIKKYEHRGIPLIYVKQISKQLLLGLDYMHRRCGIIHTDIKPENVLMEIGDVEGIVQMVEALDKQKREAKRLQRHVSRSSDITANDSSDEKWAECQTSMPCGSSSNSKSRSIEKDLSKRCFRRPRRHTIITGSQPLPSPISSSNFFEMRAHFCGSSHNSFSSVSGNRNIPSSINNNSINNGIGIKNSNNSFLNSVPHSVTRMFINEDSNDNNNNDNSKNKNNNNNNSNNNNNEDIMNTPLHEEQLADSLSTFDISNISQSSDTNGPYISNTMDSNSNVSTDINSPENLIQIKIADLGNACWYDEHYTNSIQTREYRSPEVLLGAPWGCGADIWSTACLIFELITGDFLFEPDEGHSYTKDDDHIAQIIELLGELPSYLLRNGKYTRTFFNSRGLLRNISKLKFWPLEDVLTEKYKFSKDEAKEISDFLSPMLQLDPRKRADAGGLVNHPWLKDTLGMEEIRVPDRELYGSGSDIPGWFEEVR 737
               SCOP domains d1q8ya_ A: Sky1p                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1q8yA01 A:144-211,A:226-248 Phosphorylase Kinase; domain 1          1q8yA02       1q8yA01                1q8yA02 A:212-225,A:249-735 Transferase(Phosphotransferase                                                                                                                                                                                                                                        ) domain 1                                                                                                                                                                                           -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........ee....eeeeeeeee...eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh......eeeeeee..eeeeeeee....eehhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee....hhh.eeeeeee----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....eeeeee......ee..........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....---------hhhhhhhhhhhhhh..hhhhhhhh.hhhhhh..--...........hhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------PROTEIN_KINASE_ATP      ------------------------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:144-737 (gaps) UniProt: 1-742 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Transcript 1
                 1q8y A 144 YHPAFKGEPYKDARYILVRKLGWGHFSTVWLAKDMVNNTHVAMKIVRGDKVYTEAAEDEIKLLQRVNDADNTKEDSMGANHILKLLDHFNHKGPNGVHVVMVFEVLGENLLALIKKYEHRGIPLIYVKQISKQLLLGLDYMHRRCGIIHTDIKPENVLMEIVD----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SPENLIQIKIADLGNACWYDEHYTNSIQTREYRSPEVLLGAPWGCGADIWSTACLIFELITGDFLF---------KDDDHIAQIIELLGELPSYLLRNGKYTRTFFNS--LLRNISKLKFWPLEDVLTEKYKFSKDEAKEISDFLSPMLQLDPRKRADAGGLVNHPWLKDTLGMEEIRVPDRELYGSGSDIPGWFEEVR 737
                                   153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303  |      -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -     | 543       553       563       573       583       593       603|        -|      623       633       643  |  | 653       663       673       683       693       703       713       723       733    
                                                                                                                                                                                            306                                                                                                                                                                                                                                      539                                                              604       614                             646  |                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   649                                                                                        

Chain B from PDB  Type:PROTEIN  Length:357
 aligned with SKY1_YEAST | Q03656 from UniProtKB/Swiss-Prot  Length:742

    Alignment length:592
                                   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       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735  
           SKY1_YEAST   146 PAFKGEPYKDARYILVRKLGWGHFSTVWLAKDMVNNTHVAMKIVRGDKVYTEAAEDEIKLLQRVNDADNTKEDSMGANHILKLLDHFNHKGPNGVHVVMVFEVLGENLLALIKKYEHRGIPLIYVKQISKQLLLGLDYMHRRCGIIHTDIKPENVLMEIGDVEGIVQMVEALDKQKREAKRLQRHVSRSSDITANDSSDEKWAECQTSMPCGSSSNSKSRSIEKDLSKRCFRRPRRHTIITGSQPLPSPISSSNFFEMRAHFCGSSHNSFSSVSGNRNIPSSINNNSINNGIGIKNSNNSFLNSVPHSVTRMFINEDSNDNNNNDNSKNKNNNNNNSNNNNNEDIMNTPLHEEQLADSLSTFDISNISQSSDTNGPYISNTMDSNSNVSTDINSPENLIQIKIADLGNACWYDEHYTNSIQTREYRSPEVLLGAPWGCGADIWSTACLIFELITGDFLFEPDEGHSYTKDDDHIAQIIELLGELPSYLLRNGKYTRTFFNSRGLLRNISKLKFWPLEDVLTEKYKFSKDEAKEISDFLSPMLQLDPRKRADAGGLVNHPWLKDTLGMEEIRVPDRELYGSGSDIPGWFEEVR 737
               SCOP domains d1q8yb_ B: Sky1p                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1q8yB01 B:146-211,B:   226-248 Phosphorylase Kinase; domain 1     1q8yB02       1q8yB01                1q8yB02 B:212-225,B:249-735 Transferase(Phosphotransferase                                                                                                                                                                                                                                        ) domain 1                                                                                                                                                                                           -- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pkinase-1q8yB01 B:539-706                                                                                                                                               ------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pkinase-1q8yB02 B:539-706                                                                                                                                               ------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pkinase-1q8yB03 B:539-706                                                                                                                                               ------------------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pkinase-1q8yB04 B:539-706                                                                                                                                               ------------------------------- Pfam domains (4)
         Sec.struct. author ......ee....eeeeeeee---.eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh......eeeeee....eeeeeeee....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee....hhh.eeeeeee----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------hhhheeeeee.hhhhhee..........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh..hhhhhhhh.hhhhhh...............hhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.................hhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------PROTEIN_KINASE_ATP      ------------------------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:146-737 (gaps) UniProt: 1-742 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Transcript 1
                 1q8y B 146 PAFKGEPYKDARYILVRKLG---FSTVWLAKDMVNNTHVAMKIVRGDKVYTEAAEDEIKLLQRVNDADNTKEDSMGANHILKLLDHFNHKGPNGVHVVMVFEVLGENLLALIKKYEHRGIPLIYVKQISKQLLLGLDYMHRRCGIIHTDIKPENVLMEIVD----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SPENLIQIKIADLGNACWYDEHYTNSIQTREYRSPEVLLGAPWGCGADIWSTACLIFELITGDFLFEPDEGHSYTKDDDHIAQIIELLGELPSYLLRNGKYTRTFFNSRGLLRNISKLKFWPLEDVLTEKYKFSKDEAKEISDFLSPMLQLDPRKRADAGGLVNHPWLKDTLGMEEIRVPDRELYGSGSDIPGWFEEVR 737
                                   155       165   |   175       185       195       205       215       225       235       245       255       265       275       285       295       305|        -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -   |   545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735  
                                             165 169                                                                                                                                      306                                                                                                                                                                                                                                      539                                                                                                                                                                                                      

   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, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SKY1_YEAST | Q03656)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    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.
biological process
    GO:0030003    cellular cation homeostasis    Any process involved in the maintenance of an internal steady state of cations at the level of a cell.
    GO:0006873    cellular ion homeostasis    Any process involved in the maintenance of an internal steady state of ions at the level of a cell.
    GO:0006376    mRNA splice site selection    Selection of a splice site by components of the assembling spliceosome.
    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:0042307    positive regulation of protein import into nucleus    Any process that activates or increases the frequency, rate or extent of movement of proteins from the cytoplasm into the nucleus.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SKY1_YEAST | Q036561how 1q8z 1q97 1q99 2jd5

(-) Related Entries Specified in the PDB File

1q8z 1q97 1q99