The MORPHEEINS Database

Please note: this version of the MORPHEEINS Database is still functional, but it is out of date. A new version is being developed. For more information, contact Eileen.Jaffe@fccc.edu

 

Table of Contents:
  1. Porphobilinogen synthase
  2. Pseudomonas aeruginosa GDP-Mannose dehydrogenase
  3. Bacillus subtilis HPr (histidine containing phosphocarrier protein)
  4. Mammalian CoA transferase
  5. Purine nucleoside phosphorylase
  6. Mammalian ribonucleotide reductase
  7. Peroxiredoxins
  8. Ribonuclease A
 
Name Porphobilinogen synthase
CAS 9036-37-7
EC 4.2.1.24
Reaction BRENDA
Map KEGG
GenBank NP_000022
delta-aminolevulinic acid dehydratase isoform b [Homo sapiens].
PDB 1PV8
1E51
All EC 4.2.1.24
Reference
  1. PubMed
    Jaffe, E.K.
    Morpheeins--a new structural paradigm for allosteric regulation.
    Trends Biochem Sci, 2005. 30(9): p. 490-7.
  2. PubMed
    Breinig S, Kervinen J, Stith L, Wasson AS, Fairman R, Wlodawer A, Zdanov A, Jaffe EK.
    Control of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen synthase.
    Nat Struct Biol, 2003. 10(9): p. 757-63.
  3. PubMed
    Tang L, Breinig S, Stith L, Mischel A, Tannir J, Kokona B, Fairman R, Jaffe EK.
    Single amino acid mutations alter the distribution of human porphobilinogen synthase quaternary structure isoforms (morpheeins).
    J Biol Chem, 2005.
  4. PubMed
    Tang, L., L. Stith, and E.K. Jaffe
    Substrate-induced interconversion of protein quaternary structure isoforms.
    J Biol Chem, 2005. 280(16): p. 15786-93.

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Name Pseudomonas aeruginosa GDP-Mannose dehydrogenase
CAS 37250-63-8
EC 1.1.1.132
Reaction BRENDA
Map KEGG
GenBank NP_252230
GDP-mannose 6-dehydrogenase AlgD [Pseudomonas aeruginosa PAO1].
PDB 1MFZ
All EC 1.1.1.132
Reference
  1. PubMed
    Shankar S, Ye RW, Schlictman D, Chakrabarty AM
    Exopolysaccharide alginate synthesis in Pseudomonas aeruginosa: enzymology and regulation of gene expression.
    Adv Enzymol Relat Areas Mol Biol, 1995. 70: p. 221-55.
  2. PubMed
    Naught LE, Gilbert S, Imhoff R, Snook C, Beamer L, Tipton P
    Allosterism and cooperativity in Pseudomonas aeruginosa GDP-mannose dehydrogenase.
    Biochemistry, 2002. 41(30): p. 9637-45.
  3. PubMed
    Roychoudhury S, May TB, Gill JF, Singh SK, Feingold DS, Chakrabarty AM.
    Purification and characterization of guanosine diphospho-Dmannose dehydrogenase. A key enzyme in the biosynthesis of alginate by Pseudomonas aeruginosa.
    J Biol Chem, 1989. 264(16): p. 9380-5.
  4. PubMed
    Snook, C.F., P.A. Tipton, and L.J. Beamer
    Crystal structure of GDP-mannose dehydrogenase: a key enzyme of alginate biosynthesis in P. aeruginosa.
    Biochemistry, 2003. 42(16): p. 4658-68.

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Name Bacillus subtilis HPr (histidine containing phosphocarrier protein)
CAS  
EC 2.7.1.-/3.1.3.-
Reaction  
Map  
GenBank NP_391380
HPr kinase/phosphorylase [Bacillus subtilis subsp. subtilis str. 168].
PDB 1JB1
1KO7
1KNX
All EC 2.7.1.-/3.1.3.-
Reference
  1. PubMed
    Poncet S, Mijakovic I, Nessler S, Gueguen-Chaignon V, Chaptal V, Galinier A, Boel G, Maze A, Deutscher J.
    HPr kinase/phosphorylase, a Walker motif A-containing bifunctional sensor enzyme controlling catabolite repression in Gram-positive bacteria.
    Biochim Biophys Acta, 2004. 1697(1-2): p. 123-35.
  2. PubMed
    Fieulaine S, Morera S, Poncet S, Monedero V, Gueguen-Chaignon V, Galinier A, Janin J, Deutscher J, Nessler S.
    X-ray structure of HPr kinase: a bacterial protein kinase with a Ploop nucleotide-binding domain.
    Embo J, 2001. 20(15): p. 3917-27.
  3. PubMed
    Marquez JA, Hasenbein S, Koch B, Fieulaine S, Nessler S, Russell RB, Hengstenberg W, Scheffzek K.
    Structure of the full-length HPr kinase/phosphatase from Staphylococcus xylosus at 1.95 A resolution: Mimicking the product/substrate of the phospho transfer reactions.
    Proc Natl Acad Sci U S A, 2002. 99(6): p. 3458-63.
  4. PubMed
    Allen GS, Steinhauer K, Hillen W, Stulke J, Brennan RG.
    Crystal structure of HPr kinase/phosphatase from Mycoplasma pneumoniae.
    J Mol Biol, 2003. 326(4): p. 1203-17.
  5. PubMed
    Ramstrom H, Sanglier S, Leize-Wagner E, Philippe C, Van Dorsselaer A, Haiech J.
    Properties and regulation of the bifunctional enzyme HPr kinase/phosphatase in Bacillus subtilis.
    J Biol Chem, 2003. 278(2): p. 1174-85.
  6. PubMed
    Jault JM, Fieulaine S, Nessler S, Gonzalo P, Di Pietro A, Deutscher J, Galinier A.
    The HPr kinase from Bacillus subtilis is a homo-oligomeric enzyme which exhibits strong positive cooperativity for nucleotide and fructose 1,6-bisphosphate binding.
    J Biol Chem, 2000. 275(3): p. 1773-80.

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Name Mammalian CoA transferase
CAS 9027-43-4
EC 2.8.3.5
Reaction BRENDA
Map KEGG:map00072
KEGG:map00280
KEGG:map00650
GenBank NP_999103
succinyl-CoA:alpha-ketoacid coenzyme A transferase [Sus scrofa].
PDB 1OOY
1M3E
All EC 2.8.3.5
Reference
  1. PubMed
    Rochet JC, Brownie ER, Oikawa K, Hicks LD, Fraser ME, James MN, Kay CM, Bridger WA, Wolodko WT.
    Pig heart CoA transferase exists as two oligomeric forms separated by a large kinetic barrier.
    Biochemistry, 2000. 39(37): p. 11291-302.
  2. PubMed
    Coros AM, Swenson L, Wolodko WT, Fraser ME.
    Structure of the CoA transferase from pig heart to 1.7 A resolution.
    Acta Crystallogr D Biol Crystallogr, 2004. 60(Pt 10): p. 1717-25.

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Name Purine nucleoside phosphorylase
CAS 9030-21-1
EC 2.4.2.1
Reaction BRENDA
Map KEGG:map00230
KEGG:map00240
KEGG:map00760
GenBank NP_001007819
Purine nucleoside phosphorylase [Bos taurus].
PDB 1VFN
1A69
1B8O
All EC 2.4.2.1
Reference
  1. PubMed
    Bzowska, A., E. Kulikowska, and D. Shugar
    Purine nucleoside phosphorylases: properties, functions, and clinical aspects.
    Pharmacol Ther, 2000. 88(3): p. 349-425.
  2. PubMed
    Porter, D.J.
    Purine nucleoside phosphorylase. Kinetic mechanism of the enzyme from calf spleen.
    J Biol Chem, 1992. 267(11): p. 7342-51.
  3. Wielgus-Kutrowska, B.
    Purine nucleoside phosphorylase - physicochemical properties and mechanism of interaction with ligands.
    1999, University of Warsaw
  4. PubMed
    Bzowska A, Luic M, Schroder W, Shugar D, Saenger W, Koellner G.
    Calf spleen purine nucleoside phosphorylase: purification, sequence and crystal structure of its complex with an N(7)-acycloguanosine inhibitor.
    FEBS Lett, 1995. 367(3): p. 214-8.
  5. PubMed
    Fedorov A, Shi W, Kicska G, Fedorov E, Tyler PC, Furneaux RH, Hanson JC, Gainsford GJ, Larese JZ, Schramm VL, Almo SC.
    Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis.
    Biochemistry, 2001. 40(4): p. 853-60.
  6. PubMed
    Koellner G, Luic M, Shugar D, Saenger W, Bzowska A.
    Crystal structure of the ternary complex of E. coli purine nucleoside phosphorylase with formycin B, a structural analogue of the substrate inosine, and phosphate (Sulphate) at 2.1 A resolution.
    J Mol Biol, 1998. 280(1): p. 153-66.

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Name Mammalian ribonucleotide reductase
CAS 9047-64-7
EC 1.17.4.1
Reaction BRENDA
Map KEGG:map00230
KEGG:map00240
GenBank ZP_00706346
COG0209: Ribonucleotide reductase, alpha subunit [Escherichia coli HS].
NP_001024
Ribonucleoside-diphosphate reductase M1 chain [Homo sapiens].
PDB 1RLR
All EC 1.17.4.1
Reference
  1. PubMed
    Kashlan OB, Scott CP, Lear JD, Cooperman BS.
    A comprehensive model for the allosteric regulation of mammalian ribonucleotide reductase. Functional consequences of ATP- and dATP-induced oligomerization of the large subunit.
    Biochemistry, 2002. 41(2): p. 462-74.
  2. PubMed
    Kashlan, O.B. and B.S. Cooperman
    Comprehensive model for allosteric regulation of mammalian ribonucleotide reductase: refinements and consequences.
    Biochemistry, 2003. 42(6): p. 1696-706.
  3. PubMed
    Eriksson M, Uhlin U, Ramaswamy S, Ekberg M, Regnstrom K, Sjoberg BM, Eklund H.
    Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding.
    Structure, 1997. 5(8): p. 1077-92.

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Name Peroxiredoxins
CAS  
EC 1.6.4.-
Reaction  
Map  
GenBank NP_455184
alkyl hydroperoxide reductase c22 protein [Salmonella enterica subsp. enterica serovar Typhi str. CT18].
PDB 1YEX
All EC 2.7.1.-/3.1.3.-
Reference
  1. PubMed
    Wood ZA, Poole LB, Hantgan RR, Karplus PA.
    Dimers to doughnuts: redox-sensitive oligomerization of 2-cysteine peroxiredoxins.
    Biochemistry, 2002. 41(17): p. 5493-504.
  2. PubMed
    Poole, L.B.
    Bacterial defenses against oxidants: mechanistic features of cysteine-based peroxidases and their flavoprotein reductases.
    Arch Biochem Biophys, 2005. 433(1): p. 240-54.

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Name Ribonuclease A
CAS 9001-99-4
EC 3.1.27.5
Reaction BRENDA
Map  
GenBank NP_001014408
Ribonuclease [Bos taurus].
PDB 1A2W
1F0V
1JS0
All EC 3.1.27.5
Reference
  1. PubMed
    Liu, Y. and D. Eisenberg
    3D domain swapping: as domains continue to swap.
    Protein Sci, 2002. 11(6): p. 1285-99.
  2. PubMed
    Wlodawer, A., R. Bott, and L. Sjolin
    The refined crystal structure of ribonuclease A at 2.0 A resolution.
    J Biol Chem, 1982. 257(3): p. 1325-32.
  3. PubMed
    Liu Y, Hart PJ, Schlunegger MP, Eisenberg D.
    The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1- A resolution.
    Proc Natl Acad Sci U S A, 1998. 95(7): p. 3437-42.
  4. PubMed
    Liu Y, Gotte G, Libonati M, Eisenberg D.
    A domain-swapped RNase A dimer with implications for amyloid formation.
    Nat Struct Biol, 2001. 8(3): p. 211-4.
  5. PubMed
    Liu Y, Gotte G, Libonati M, Eisenberg D.
    Structures of the two 3D domain-swapped RNase A trimers.
    Protein Sci, 2002. 11(2): p. 371-80.
  6. PubMed
    Gotte, G., M. Bertoldi, and M. Libonati
    Structural versatility of bovine ribonuclease A. Distinct conformers of trimeric and tetrameric aggregates of the enzyme.
    Eur J Biochem, 1999. 265(2): p. 680-7.

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