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(-) Description

Title :  THE X-RAY CRYSTAL STRUCTURE OF SKY1P, AN SR PROTEIN KINASE IN YEAST
 
Authors :  B. J. Nolen, C. Y. Yun, C. F. Wong, J. A. Mccammon, X. -D. Fu, G. Ghosh
Date :  11 Dec 00  (Deposition) - 28 Feb 01  (Release) - 02 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nolen, C. Y. Yun, C. F. Wong, J. A. Mccammon, X. D. Fu, G. Ghosh
The Structure Of Sky1P Reveals A Novel Mechanism For Constitutive Activity.
Nat. Struct. Biol. V. 8 176 2001
PubMed-ID: 11175909  |  Reference-DOI: 10.1038/84178
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE YMR216C
    Chains: A
    EC Number: 2.7.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SKY1PDELTANS
    Gene: YMR216C
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2SO46Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:154 , ASP A:155 , PHE A:232 , HIS A:234 , LYS A:235 , HOH A:774 , HOH A:799 , HOH A:819 , HOH A:935BINDING SITE FOR RESIDUE SO4 A 743
2AC2SOFTWARETYR A:632 , ARG A:635 , ARG A:692 , HOH A:854BINDING SITE FOR RESIDUE SO4 A 744
3AC3SOFTWAREGLY A:167 , HIS A:168 , PHE A:169 , SER A:170 , SO4 A:747 , HOH A:766BINDING SITE FOR RESIDUE SO4 A 745
4AC4SOFTWAREHIS A:145 , PRO A:146 , ALA A:147 , LYS A:163 , THR A:171 , TRP A:173 , HOH A:862 , HOH A:918 , HOH A:926BINDING SITE FOR RESIDUE SO4 A 746
5AC5SOFTWARESER A:170 , LYS A:187 , ALA A:199 , SO4 A:745 , HOH A:882BINDING SITE FOR RESIDUE SO4 A 747
6AC6SOFTWAREARG A:568 , ARG A:571BINDING SITE FOR RESIDUE SO4 A 748
7AC7SOFTWAREHIS A:262 , GLU A:596 , GLY A:600 , PHE A:602 , HOH A:925BINDING SITE FOR RESIDUE EDO A 749
8AC8SOFTWAREGLU A:247 , VAL A:248 , LEU A:249 , GLY A:250 , LEU A:301BINDING SITE FOR RESIDUE EDO A 750

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (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

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YMR216C1YMR216C.1XIII:701038-6988102229SKY1_YEAST1-7427421A:144-737 (gaps)594

(-) 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:346
 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 d1howa_ A: Sky1p                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1howA01 A:144-211,A:226-248 Phosphorylase Kinase; domain 1          1howA02       1howA01                1howA02 A:212-225,A:249-737 Transferase(Phosphotransferase                                                                                                                                                                                                                                        ) domain 1                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........ee....eeeeeeeee...eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh......eeeeee....eeeeeee.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee....hhh........----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....eeeeee.hhhhhee..........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......-------hhhhhhhhhhhhh..hhhhhhh........---------......hhhhhhhhh...hhhhhhhhhhhhh...........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
                1how A  144 FHPAFKGEPYKDARYILVRKLGWGHFSTVWLAKDMVNNTHVAMKIVRGDKVYTEAAEDEIKLLQRVNDADNTKEDSMGANHILKLLDHFNHKGPNGVHVVMVFEVLGENLLALIKKYEHRGIPLIYVKQISKQLLLGLDYMHRRCGIIHTDIKPENVLMEIVD----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SPENLIQIKIADLGNACWYDEHYTNSIQTREYRSPEVLLGAPWGCGADIWSTACLIFELITGDFLFEPD-------DDDHIAQIIELLGELPSYLLRNGKYTRTFF---------SKLKFWPLEDVLTEKYKFSKDEAKEISDFLSPMLQLDPRKRADAGGLVNHPWLKDTLGMEEIRVPDRELYGSGSDIPGWFEEVR  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|        -|      663       673       683       693       703       713       723       733    
                                                                                                                                                                                          304A|                                                                                                                                                                                                                                      539                                                                 607     615                          644       654                                                                                   
                                                                                                                                                                                           304B
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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 | Q03656: 1q8y 1q8z 1q97 1q99 2jd5

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