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(-) Description

Title :  STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP
 
Authors :  G. J. Schlauderer, G. E. Schulz
Date :  14 Dec 95  (Deposition) - 03 Apr 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nucleoside Monophosphate Kinase, Myokinase, Transferase (Phosphotransferase) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. J. Schlauderer, K. Proba, G. E. Schulz
Structure Of A Mutant Adenylate Kinase Ligated With An Atp-Analogue Showing Domain Closure Over Atp.
J. Mol. Biol. V. 256 223 1996
PubMed-ID: 8594191  |  Reference-DOI: 10.1006/JMBI.1996.0080
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENYLATE KINASE
    Cellular LocationCYTOSOL
    ChainsA, B
    EC Number2.7.4.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUAKYI
    Expression System StrainHB101
    Expression System Taxid562
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ATF2Ligand/IonPHOSPHODIFLUOROMETHYLPHOSPHONIC ACID-ADENYLATE ESTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:13 , GLY A:14 , ALA A:15 , GLY A:16 , LYS A:17 , GLY A:18 , THR A:19 , ARG A:128 , ARG A:132 , SER A:141 , TYR A:142 , HIS A:143 , PHE A:146 , ALA A:202 , GLN A:204 , PRO A:206 , HOH A:243 , HOH A:249 , HOH A:252 , HOH A:291 , LYS B:55 , GLN B:59 , HOH B:231BINDING SITE FOR RESIDUE ATF A 230
2AC2SOFTWARELYS A:55 , GLN A:59 , PRO B:13 , GLY B:14 , GLY B:16 , LYS B:17 , GLY B:18 , THR B:19 , ARG B:128 , ARG B:132 , SER B:141 , TYR B:142 , HIS B:143 , PHE B:146 , GLN B:204 , PRO B:205 , PRO B:206 , HOH B:261 , HOH B:289BINDING SITE FOR RESIDUE ATF B 230

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:91 -Pro A:92
2Phe B:91 -Pro B:92

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADENYLATE_KINASEPS00113 Adenylate kinase signature.KAD2_YEAST88-99
 
  2A:86-97
B:86-97

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR226W1YDR226W.1IV:916483-917151669KAD2_YEAST1-2222222A:1-220
B:1-220
220
220

(-) 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:220
 aligned with KAD2_YEAST | P07170 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
           KAD2_YEAST     3 SSESIRMVLIGPPGAGKGTQAPNLQERFHAAHLATGDMLRSQIAKGTQLGLEAKKIMDQGGLVSDDIMVNMIKDELTNNPACKNGFILDGFPRTIPQAEKLDQMLKEQGTPLEKAIELKVDDELLVARITGRLIHPASGRSYHKIFNPPKEDMKDDVTGEALVQRSDDNADALKKRLAAYHAQTEPIVDFYKKTGIWAGVDASQPPATVWADILNKLGKD 222
               SCOP domains d1dvra1 A:1-130,A:169-220 Adenylate kinase                                                                                        d1dvra2 A:131-168                     d1dvra1 A:1-130,A:169-220 Adenylate kinase           SCOP domains
               CATH domains 1dvrA00 A:1-220 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.....hhhhhhhhhhhh..eeeehhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhh.hhhh..eeee.....hhhhhhhhhhhhhh.....eeeeee..hhhhhhhhh.eeee....eeee..........................hhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------ADENYLATE_KI--------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-220 UniProt: 1-222 [INCOMPLETE]                                                                                                                                                                           Transcript 1
                 1dvr A   1 SSESIRMVLIGPPGAGKGTQAPNLQERFHAAHLATGDMLRSQIAKGTQLGLEAKKIMDQGGLVSDDIMVNMIKDELTNNPACKNGFILVGFPRTIPQAEKLDQMLKEQGTPLEKAIELKVDDELLVARITGRLIHPASGRSYHKIFNPPKEDMKDDVTGEALVQISDDNADALKKRLAAYHAQTEPIVDFYKKTGIWAGVDASQPPATVWADILNKLGKN 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with KAD2_YEAST | P07170 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
           KAD2_YEAST     3 SSESIRMVLIGPPGAGKGTQAPNLQERFHAAHLATGDMLRSQIAKGTQLGLEAKKIMDQGGLVSDDIMVNMIKDELTNNPACKNGFILDGFPRTIPQAEKLDQMLKEQGTPLEKAIELKVDDELLVARITGRLIHPASGRSYHKIFNPPKEDMKDDVTGEALVQRSDDNADALKKRLAAYHAQTEPIVDFYKKTGIWAGVDASQPPATVWADILNKLGKD 222
               SCOP domains d1dvrb1 B:1-130,B:169-220 Adenylate kinase                                                                                        d1dvrb2 B:131-168                     d1dvrb1 B:1-130,B:169-220 Adenylate kinase           SCOP domains
               CATH domains 1dvrB00 B:1-220 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....hhhhhhhhhhhh..eeeehhhhhhhhhh...hhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhheeeee.....hhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhheee......eee..........................hhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------ADENYLATE_KI--------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-220 UniProt: 1-222 [INCOMPLETE]                                                                                                                                                                           Transcript 1
                 1dvr B   1 SSESIRMVLIGPPGAGKGTQAPNLQERFHAAHLATGDMLRSQIAKGTQLGLEAKKIMDQGGLVSDDIMVNMIKDELTNNPACKNGFILVGFPRTIPQAEKLDQMLKEQGTPLEKAIELKVDDELLVARITGRLIHPASGRSYHKIFNPPKEDMKDDVTGEALVQISDDNADALKKRLAAYHAQTEPIVDFYKKTGIWAGVDASQPPATVWADILNKLGKN 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KAD2_YEAST | P07170)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004017    adenylate kinase activity    Catalysis of the reaction: ATP + AMP = 2 ADP.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0019205    nucleobase-containing compound kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP or GTP, to a nucleobase, nucleoside, nucleotide or polynucleotide substrate.
    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:0016776    phosphotransferase activity, phosphate group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a phosphate group (acceptor).
    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:0006172    ADP biosynthetic process    The chemical reactions and pathways resulting in the formation of ADP, adenosine 5'-diphosphate.
    GO:0046033    AMP metabolic process    The chemical reactions and pathways involving AMP, adenosine monophosphate.
    GO:0046034    ATP metabolic process    The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0006270    DNA replication initiation    The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
    GO:0046939    nucleotide phosphorylation    The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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        KAD2_YEAST | P071701aky 2aky 3aky

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