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CATH domain | Related DB codes (homologues) |
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3.40.50.300 : Rossmann fold | S00527,S00547,S00550,S00554,S00555,S00671,S00672,S00676,S00680,S00682,S00913,S00914,S00301,S00302,S00303,S00304,S00307,S00308,S00305,S00306,S00309,S00310,S00311,M00114,M00199,D00129,D00130,D00540,M00186 |
Enzyme Name | UniProtKB | KEGG |
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| P35028 |
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Protein name | Adenylate kinase | adenylate kinasemyokinase5'-AMP-kinaseadenylic kinaseadenylokinase |
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Synonyms | AKEC 2.7.4.3ATP-AMP transphosphorylase |
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RefSeq | YP_255258.1 (Protein) NC_007181.1 (DNA/RNA sequence)
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KEGG pathways | MAP code | Pathways |
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MAP00230 | Purine metabolism |
UniProtKB:Accession Number | P35028 |
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Entry name | KADA_SULAC |
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Activity | ATP + AMP = 2 ADP. |
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Subunit | Homotrimer. |
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Subcellular location | Cytoplasm. |
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Cofactor |
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Compound table: links to PDB-related databases & PoSSuM |
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| Cofactors | Substrates | Products |
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KEGG-id | C00305 | C00002 | C00020 | C00008 | C00008 |
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Compound | Magnesium | ATP | AMP | ADP (from ATP) | ADP (from AMP) |
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Type | divalent metal (Ca2+, Mg2+) | amine group,nucleotide | amine group,nucleotide | amine group,nucleotide | amine group,nucleotide |
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ChEBI | 18420
| 15422
| 16027
| 16761
| 16761
|
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PubChem | 888
| 5957
| 6083
| 6022
| 6022
|
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| | | | | | | | | | | | |
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1nksA |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound |
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1nksB |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound |
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1nksC |  |  |  |  |  |  |  | Unbound | Unbound | Bound:AMP | Unbound | Unbound |
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1nksD |  |  |  |  |  |  |  | Unbound | Unbound | Bound:AMP | Unbound | Unbound |
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1nksE |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound |
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1nksF |  |  |  |  |  |  |  | Unbound | Unbound | Bound:AMP | Bound:ADP | Unbound |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[9] | p.368-370 |
| [13] | Fig.5 |
| [17] | p.5545 |
| [18] | p.6810-6813 |
| [19] | p.172-175 |
| [20] | p.3181 |
| [26] | p.1266-1269 |
| [32] | p.172-174 |
|
references | [1] |
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PubMed ID | 4367210 |
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Journal | Nature |
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Year | 1974 |
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Volume | 250 |
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Pages | 120-3 |
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Authors | Schulz GE, Elzinga M, Marx F, Schrimer RH |
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Title | Three dimensional structure of adenyl kinase. |
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Related PDB | P00571 |
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[2] |
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PubMed ID | 6086335 |
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Journal | Eur J Biochem |
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Year | 1984 |
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Volume | 141 |
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Pages | 629-36 |
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Authors | Frank R, Trosin M, Tomasselli AG, Schulz GE, Schirmer RH |
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Title | Mitochondrial adenylate kinase (AK2) from bovine heart. Homology with the cytosolic isoenzyme in the catalytic region. |
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[3] |
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PubMed ID | 3002789 |
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Journal | Eur J Biochem |
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Year | 1986 |
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Volume | 154 |
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Pages | 205-11 |
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Authors | Frank R, Trosin M, Tomasselli AG, Noda L, Krauth-Siegel RL, Schirmer RH |
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Title | Mitochondrial adenylate kinase (AK2) from bovine heart. The complete primary structure. |
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[4] |
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PubMed ID | 2869483 |
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Journal | Proc Natl Acad Sci U S A |
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Year | 1986 |
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Volume | 83 |
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Pages | 907-11 |
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Authors | Fry DC, Kuby SA, Mildvan AS |
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Title | ATP-binding site of adenylate kinase: mechanistic implications of its homology with ras-encoded p21, F1-ATPase, and other nucleotide-binding proteins. |
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Related UniProtKB | P00571 |
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[5] |
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PubMed ID | 3023080 |
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Journal | Eur J Biochem |
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Year | 1986 |
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Volume | 161 |
---|
Pages | 127-32 |
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Authors | Schulz GE, Schiltz E, Tomasselli AG, Frank R, Brune M, Wittinghofer A, Schirmer RH |
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Title | Structural relationships in the adenylate kinase family. |
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[6] |
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PubMed ID | 3023140 |
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Journal | FEBS Lett |
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Year | 1986 |
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Volume | 208 |
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Pages | 301-4 |
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Authors | Dreusicke D, Schulz GE |
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Title | The glycine-rich loop of adenylate kinase forms a giant anion hole. |
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[7] |
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PubMed ID | 2821281 |
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Journal | J Mol Biol |
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Year | 1987 |
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Volume | 195 |
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Pages | 649-58 |
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Authors | Egner U, Tomasselli AG, Schulz GE |
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Title | Structure of the complex of yeast adenylate kinase with the inhibitor P1,P5-di(adenosine-5'-)pentaphosphate at 2.6 A resolution. |
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[8] |
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PubMed ID | 2851785 |
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Journal | Protein Seq Data Anal |
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Year | 1988 |
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Volume | 1 |
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Pages | 335-43 |
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Authors | Reuner C, Hable M, Wilmanns M, Kiefer E, Schiltz E, Schulz GE |
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Title | Amino acid sequence and three-dimensional structure of cytosolic adenylate kinase from carp muscle. |
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[9] |
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PubMed ID | 2832612 |
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Journal | J Mol Biol |
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Year | 1988 |
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Volume | 199 |
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Pages | 359-71 |
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Authors | Dreusicke D, Karplus PA, Schulz GE |
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Title | Refined structure of porcine cytosolic adenylate kinase at 2.1 A resolution. |
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Related PDB | 3adk |
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Related UniProtKB | P00571 |
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[10] |
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PubMed ID | 2846042 |
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Journal | Biochemistry |
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Year | 1988 |
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Volume | 27 |
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Pages | 5544-52 |
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Authors | Tian GC, Sanders CR 2nd, Kishi F, Nakazawa A, Tsai MD |
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Title | Mechanism of adenylate kinase. Histidine-36 is not directly involved in catalysis, but protects cysteine-25 and stabilizes the tertiary structure. |
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[11] |
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PubMed ID | 2845103 |
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Journal | J Mol Biol |
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Year | 1988 |
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Volume | 202 |
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Pages | 909-12 |
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Authors | Muller CW, Schulz GE |
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Title | Structure of the complex of adenylate kinase from Escherichia coli with the inhibitor P1,P5-di(adenosine-5'-)pentaphosphate. |
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[12] |
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PubMed ID | 2850368 |
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Journal | J Mol Biol |
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Year | 1988 |
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Volume | 203 |
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Pages | 1021-8 |
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Authors | Dreusicke D, Schulz GE |
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Title | The switch between two conformations of adenylate kinase. |
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[13] |
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PubMed ID | 2223776 |
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Journal | Biochemistry |
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Year | 1990 |
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Volume | 29 |
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Pages | 7451-9 |
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Authors | Reinstein J, Schlichting I, Wittinghofer A |
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Title | Structurally and catalytically important residues in the phosphate binding loop of adenylate kinase of Escherichia coli. |
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Related UniProtKB | P69441 |
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[14] |
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PubMed ID | 2162964 |
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Journal | J Mol Biol |
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Year | 1990 |
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Volume | 213 |
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Pages | 627-30 |
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Authors | Schulz GE, Muller CW, Diederichs K |
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Title | Induced-fit movements in adenylate kinases. |
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[15] |
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PubMed ID | 2175649 |
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Journal | Biochemistry |
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Year | 1990 |
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Volume | 29 |
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Pages | 8138-44 |
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Authors | Diederichs K, Schulz GE |
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Title | Three-dimensional structure of the complex between the mitochondrial matrix adenylate kinase and its substrate AMP. |
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[16] |
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PubMed ID | 1994037 |
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Journal | J Mol Biol |
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Year | 1991 |
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Volume | 217 |
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Pages | 541-9 |
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Authors | Diederichs K, Schulz GE |
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Title | The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 A resolution. |
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[17] |
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PubMed ID | 2036423 |
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Journal | Biochemistry |
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Year | 1991 |
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Volume | 30 |
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Pages | 5539-46 |
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Authors | Yan HG, Tsai MD |
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Title | Mechanism of adenylate kinase. Demonstration of a functional relationship between aspartate 93 and Mg2+ by site-directed mutagenesis and proton, phosphorus-31, and magnesium-25 NMR. |
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[18] |
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PubMed ID | 2069947 |
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Journal | Biochemistry |
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Year | 1991 |
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Volume | 30 |
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Pages | 6806-18 |
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Authors | Tsai MD, Yan HG |
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Title | Mechanism of adenylate kinase: site-directed mutagenesis versus X-ray and NMR. |
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[19] |
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PubMed ID | 1548697 |
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Journal | J Mol Biol |
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Year | 1992 |
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Volume | 224 |
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Pages | 159-77 |
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Authors | Muller CW, Schulz GE |
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Title | Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state. |
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Related PDB | 1ake |
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Related UniProtKB | P69441 |
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[20] |
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PubMed ID | 8451239 |
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Journal | Proteins |
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Year | 1993 |
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Volume | 15 |
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Pages | 42-9 |
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Authors | Muller CW, Schulz GE |
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Title | Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop. |
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Related PDB | 1e4v,1e4y |
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Related UniProtKB | P69441 |
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[21] |
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PubMed ID | 8429559 |
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Journal | J Mol Biol |
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Year | 1993 |
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Volume | 229 |
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Pages | 494-501 |
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Authors | Gerstein M, Schulz G, Chothia C |
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Title | Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers. |
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[22] |
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PubMed ID | 7880812 |
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Journal | Biochemistry |
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Year | 1995 |
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Volume | 34 |
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Pages | 3172-82 |
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Authors | Byeon L, Shi Z, Tsai MD |
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Title | Mechanism of adenylate kinase. The "essential lysine" helps to orient the phosphates and the active site residues to proper conformations. |
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[23] |
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PubMed ID | 7937733 |
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Journal | Proteins |
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Year | 1994 |
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Volume | 19 |
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Pages | 183-98 |
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Authors | Berry MB, Meador B, Bilderback T, Liang P, Glaser M, Phillips GN Jr |
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Title | The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP. |
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Related PDB | 1ank,1eck,2eck |
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[24] |
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PubMed ID | 7663945 |
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Journal | Structure |
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Year | 1995 |
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Volume | 3 |
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Pages | 483-90 |
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Authors | Vonrhein C, Schlauderer GJ, Schulz GE |
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Title | Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. |
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[25] |
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PubMed ID | 7635152 |
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Journal | Eur J Biochem |
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Year | 1995 |
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Volume | 231 |
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Pages | 405-13 |
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Authors | Spuergin P, Abele U, Schulz GE |
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Title | Stability, activity and structure of adenylate kinase mutants. |
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Related PDB | 3aky |
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[26] |
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PubMed ID | 7670369 |
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Journal | Protein Sci |
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Year | 1995 |
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Volume | 4 |
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Pages | 1262-71 |
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Authors | Abele U, Schulz GE |
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Title | High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer. |
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Related PDB | 1aky,2aky |
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Related UniProtKB | P07170 |
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[27] |
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PubMed ID | 8805521 |
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Journal | Structure |
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Year | 1996 |
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Volume | 4 |
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Pages | 147-56 |
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Authors | Muller CW, Schlauderer GJ, Reinstein J, Schulz GE |
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Title | Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding. |
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Related PDB | 4ake |
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[28] |
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PubMed ID | 8594191 |
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Journal | J Mol Biol |
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Year | 1996 |
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Volume | 256 |
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Pages | 223-7 |
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Authors | Schlauderer GJ, Proba K, Schulz GE |
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Title | Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP. |
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Related PDB | 1dvr |
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[29] |
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PubMed ID | 8868479 |
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Journal | Protein Sci |
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Year | 1996 |
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Volume | 5 |
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Pages | 434-41 |
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Authors | Schlauderer GJ, Schulz GE |
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Title | The structure of bovine mitochondrial adenylate kinase: comparison with isoenzymes in other compartments. |
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Related PDB | 1ak2,2ak2 |
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Related UniProtKB | P08166 |
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[30] |
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PubMed ID | 9428681 |
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Journal | Eur J Biochem |
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Year | 1997 |
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Volume | 250 |
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Pages | 326-31 |
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Authors | Wild K, Grafmuller R, Wagner E, Schulz GE |
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Title | Structure, catalysis and supramolecular assembly of adenylate kinase from maize. |
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[31] |
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PubMed ID | 9715904 |
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Journal | Proteins |
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Year | 1998 |
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Volume | 32 |
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Pages | 276-88 |
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Authors | Berry MB, Phillips GN Jr |
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Title | Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+. |
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Related PDB | 1zio,1zip,1zin |
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Related UniProtKB | P27142 |
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[32] |
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PubMed ID | 9733648 |
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Journal | J Mol Biol |
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Year | 1998 |
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Volume | 282 |
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Pages | 167-79 |
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Authors | Vonrhein C, Bonisch H, Schafer G, Schulz GE |
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Title | The structure of a trimeric archaeal adenylate kinase. |
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Related PDB | 1nks |
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Related UniProtKB | P35028 |
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[33] |
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PubMed ID | 9844727 |
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Journal | Biochem Mol Biol Int |
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Year | 1998 |
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Volume | 46 |
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Pages | 673-80 |
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Authors | Ayabe T, Park SK, Nagahama H, Maruyama H, Sumida M, Takenaka H, Takenaka O, Onitsuka T, Hamada M |
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Title | Site-directed mutagenesis and steady-state kinetic analysis of mutant enzymes of human adenylate kinase. |
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[34] |
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PubMed ID | 10491122 |
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Journal | Eur J Biochem |
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Year | 1999 |
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Volume | 264 |
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Pages | 765-74 |
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Authors | Burlacu-Miron S, Gilles AM, Popescu A, Barzu O, Craescu CT |
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Title | Multinuclear magnetic resonance studies of Escherichia coli adenylate kinase in free and bound forms. Resonance assignment, secondary structure and ligand binding. |
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[35] |
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PubMed ID | 11976328 |
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Journal | J Biol Chem |
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Year | 2002 |
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Volume | 277 |
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Pages | 25685-91 |
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Authors | Addona GH, Husain SS, Stehle T, Miller KW |
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Title | Geometric isomers of a photoactivable general anesthetic delineate a binding site on adenylate kinase. |
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comments | This enzyme is homologous to the counterpart enzymes (see S00305 and S00547 in EzCatDB). This enzyme from archaean species (PDB; 1nks) seems to be distinct from others, and catalytic residues are not so conserved (see [32]). The literature [12], [14], [21], [23], [24] & [27] reported that conformational change occurs upon substrate binding and during catalysis. The transfer reaction of the gamma-phosphoryl group of ATP occurs by an in-line mechanism involving a tentacovalent-transition-state with the nucleophilic acceptor group, the oxygen atom of the phosphate group of AMP, and the leaving group, the beta-phosphate of ATP in the two apical positions (see [19]). The paper [26] suggested that the in-line phosphoryl transfer is associative (SN2-like). The transferred phosphoryl group is stabilized by conserved residues, Lys14, and Arg139. The acceptor phosphoryl group is stabilized by Arg54 and His93. The role of cofactor, magnesium ion, which is bound to Asp91, is discussed in the papers [17] & [31], as follows: (1) This ion shield the negative charge of the transferred group, the gamma-phosphate of ATP from the attacking nucleophile, the acceptor oxygen atom of the alpha-phosphate of AMP, by its interaction with the gamma-phosphate. (2) This ion enhances the cleavage of the P(gamma)-O bond by electrophilic effects. (3) This ion orients the phosphate chain in proper positions.
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created | updated |
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2002-05-31 | 2010-05-20 |
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