Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THE CATALYTIC MECHANISM OF PHOSPHORYLASE KINASE PROBED BY MUTATIONAL STUDIES
 
Authors :  V. T. Skamnaki, D. J. Owen, M. E. M. Noble, E. D. Lowe, N. G. Oikonomakos, L. N. Johnson
Date :  24 Aug 99  (Deposition) - 14 Dec 99  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase (Glycogen Metabolism), Glycogen Metabolism, Transferase, Serine/Threonine-Protein, Kinase, Atp-Binding, Calmodulin-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. T. Skamnaki, D. J. Owen, M. E. Noble, E. D. Lowe, G. Lowe, N. G. Oikonomakos, L. N. Johnson
Catalytic Mechanism Of Phosphorylase Kinase Probed By Mutational Studies.
Biochemistry V. 38 14718 1999
PubMed-ID: 10545198  |  Reference-DOI: 10.1021/BI991454F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORYLASE KINASE
    ChainsA
    EC Number2.7.1.38
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMW172
    Expression System Taxid562
    FragmentGAMMA SUBUNIT, TRUNCATED TO RESIDUES 1 - 298
    MutationYES
    Organism CommonRABBIT
    Organism ScientificORYCTOLAGUS CUNICULUS
    Organism Taxid9986
    Other DetailsLIGANDS ATP AND MN(II)
    SynonymRABBIT MUSCLE PHOSPHORYLASE KINASE
    TissueSKELETAL MUSCLE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MN2Ligand/IonMANGANESE (II) ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:167 , ATP A:301 , HOH A:467BINDING SITE FOR RESIDUE MN B 382
2AC2SOFTWAREASN A:154 , ASP A:167 , ATP A:301 , HOH A:402BINDING SITE FOR RESIDUE MN B 383
3AC3SOFTWARELYS A:72 , ARG A:148 , LEU A:180 , HOH A:448 , HOH A:415BINDING SITE FOR RESIDUE SO4 C 401
4AC4SOFTWARELEU A:25 , GLY A:26 , GLY A:28 , SER A:31 , VAL A:33 , ALA A:46 , LYS A:48 , ASP A:104 , MET A:106 , GLU A:110 , LYS A:124 , GLU A:153 , ASN A:154 , LEU A:156 , ASP A:167 , MN A:302 , MN A:303 , HOH A:447 , HOH A:422 , HOH A:402BINDING SITE FOR RESIDUE ATP B 381

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QL6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QL6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QL6)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PHKG1_RABIT26-49  1A:25-48
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.PHKG1_RABIT146-158  1A:145-157

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSOCUT000000136151ENSOCUE00000243534Un0090:781787-78184761PHKG1_RABIT-00--
1.2ENSOCUT000000136152ENSOCUE00000222370Un0090:784235-784336102PHKG1_RABIT1-28281A:11-2717
1.3ENSOCUT000000136153ENSOCUE00000159051Un0090:785464-785648185PHKG1_RABIT28-90631A:27-8963
1.4ENSOCUT000000136154ENSOCUE00000292633Un0090:785983-78603755PHKG1_RABIT90-108191A:89-10719
1.5ENSOCUT000000136155ENSOCUE00000159073Un0090:787798-78786366PHKG1_RABIT108-130231A:107-12923
1.6ENSOCUT000000136156ENSOCUE00000159085Un0090:787992-788155164PHKG1_RABIT130-185561A:129-18456
1.7ENSOCUT000000136157ENSOCUE00000247647Un0090:788562-78865291PHKG1_RABIT185-215311A:184-21431
1.8ENSOCUT000000136158ENSOCUE00000159109Un0090:788761-788914154PHKG1_RABIT215-266521A:214-26552
1.9ENSOCUT000000136159ENSOCUE00000159120Un0090:789079-789204126PHKG1_RABIT267-308421A:266-29126
1.10ENSOCUT0000001361510ENSOCUE00000159128Un0090:789525-790385861PHKG1_RABIT309-389810--

(-) 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:281
 aligned with PHKG1_RABIT | P00518 from UniProtKB/Swiss-Prot  Length:387

    Alignment length:281
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291 
          PHKG1_RABIT    12 STHGFYENYEPKEILGRGVSSVVRRCIHKPTCKEYAVKIIDVTGGGSFSAEEVQELREATLKEVDILRKVSGHPNIIQLKDTYETNTFFFLVFDLMKKGELFDYLTEKVTLSEKETRKIMRALLEVICALHKLNIVHRDLKPENILLDDDMNIKLTDFGFSCQLDPGEKLREVCGTPSYLAPEIIECSMNDNHPGYGKEVDMWSTGVIMYTLLAGSPPFWHRKQMLMLRMIMSGNYQFGSPEWDDYSDTVKDLVSRFLVVQPQKRYTAEEALAHPFFQQYV 292
               SCOP domains d1ql6a_ A: gamma-subunit of glycogen phosphorylase kinase (Phk)                                                                                                                                                                                                                           SCOP domains
               CATH domains ----1ql6A01 A:15-105 Phosphorylase Kinase; domain 1                                            1ql6A02 A:106-291 Transferase(Phosphotransferase) domain 1                                                                                                                                 CATH domains
               Pfam domains --------Pkinase-1ql6A01 A:19-287                                                                                                                                                                                                                                                     ---- Pfam domains
         Sec.struct. author hhhhhhhheee..eeee...eeeeeeee....eeeeeeeee........hhhhhhhhhhhhhhhhhhhhh........eeeeee...eeeeeee......hhhhhhhh....hhhhhhhhhhhhhhhhhhhh.........hhheee.....eee.....................hhh..hhhhhhhh........hhhhhhhhhhhhhhhhh.........hhhhhhhhhh.........hhh..hhhhhhhhhh....hhh...hhhhhh.hhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PROTEIN_KINASE_ATP      ------------------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2         -------------------------------------------------------------Exon 1.4           ---------------------Exon 1.6  PDB: A:129-184 UniProt: 130-185               -----------------------------Exon 1.8  PDB: A:214-265 UniProt: 215-266           Exon 1.9  PDB: A:266-291   Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.3  PDB: A:27-89 UniProt: 28-90                          -----------------Exon 1.5  PDB: A:107-12------------------------------------------------------Exon 1.7  PDB: A:184-214       ----------------------------------------------------------------------------- Transcript 1 (2)
                 1ql6 A  11 STHGFYENYEPKEILGRGVSSVVRRCIHKPTCKEYAVKIIDVTGGGSFSAEEVQELREATLKEVDILRKVSGHPNIIQLKDTYETNTFFFLVFDLMKKGELFDYLTEKVTLSEKETRKIMRALLEVICALHKLNIVHRDLKPENILLDDDMNIKLTDFGFSCQLDPGEKLRSVCGTPSYLAPEIIECSMNDNHPGYGKEVDMWSTGVIMYTLLAGSPPFWHRKQMLMLRMIMSGNYQFGSPEWDDYSDTVKDLVSRFLVVQPQKRYTAEEALAHPFFQQYV 291
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PHKG1_RABIT | P00518)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    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:0004689    phosphorylase kinase activity    Catalysis of the reaction: 4 ATP + 2 phosphorylase b = 4 ADP + phosphorylase a.
    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:0050321    tau-protein kinase activity    Catalysis of the reaction: ATP + tau-protein = ADP + O-phospho-tau-protein.
    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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0005978    glycogen biosynthetic process    The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.
    GO:0005977    glycogen metabolic process    The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0005964    phosphorylase kinase complex    An enzyme complex that catalyzes the phosphorylation of phosphorylase b to form phosphorylase a.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ql6)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ql6
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PHKG1_RABIT | P00518
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.38
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PHKG1_RABIT | P00518
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PHKG1_RABIT | P005181phk 2phk

(-) Related Entries Specified in the PDB File

1phk TWO STRUCTURES OF THE CATALYTIC DOMAIN OF PHOSPHORYLASE, KINASE: AN ACTIVE PROTEIN KINASE COMPLEXED WITH NUCLEOTIDE, SUBSTRATE-ANALOGUE AND PRODUCT
2phk THE CRYSTAL STRUCTURE OF A PHOSPHORYLASE KINASE PEPTIDE SUBSTRATE COMPLEX: KINASE SUBSTRATE RECOGNITION