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Bioinformatics Analysis of YqjG : an introduction and some questions

Bioinformatics Analysis of YqjG : an introduction and some questions. YqjG : “Uncharacterized protein” from Escherichia coli UniProt ID = P42620 (YQJG_ECOLI) GenBank GI = 1176792 General annotation from UniProt : Belongs to the GST superfamily. Omega family.

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Bioinformatics Analysis of YqjG : an introduction and some questions

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  1. Bioinformatics Analysis of YqjG:an introduction and some questions YqjG: “Uncharacterized protein” from Escherichia coli UniProt ID = P42620 (YQJG_ECOLI) GenBank GI = 1176792 General annotation from UniProt: Belongs to the GST superfamily. Omega family. Contains 1 GST C-terminal domain.

  2. Network Generated by S. Brown – August 2010 Nu YGHU_ECOLI • Close Up of the Cluster – 96 sequences • YqjG in black • Escherichia coli K-12 • 328 amino acids, 37.4 kD • Annotated as being part of the omega class • Q8NR03 in pink • Corynebacteriumglutamicum • 3M1G structure Beta EGST_ECOLI Zeta GSTA1_HUMAN Phi GSTF1_MAIZE Theta GSTT1_HUMAN Tau GSTU1_ORYSJ Omega GSTO1_HUMAN Alpha GSTA3_CHICK Sigma GST_OMMSL Pi GSTP_ONCVO • Overall sequence similarity network containing 2,851 sequences and 97,144 edges. • Edges represent BLAST e-values of 1e-18 or more significance. • Large nodes are colored by the classification of the amino acid sequence in SWISS-PROT and indicate a representative member of each subgroup. Mu GSTM1_RAT

  3. Structural Similarity to Omega Class GSTs PDB Code 1EEM Omega class glutathione transferase from homo sapiens YqjG a Glutathione Transferase from Escherichia coli Subunit 1 (teal, blue) : Subunit 2 (pink/red) Subunit 1 (green/lemon) : Subunit 2 (teal,blue)

  4. Dimer Interface Formation in the Omega Class Alpha Helix A Alpha Helix 3 Subunit 1 (teal, blue) : Subunit 2 (pink/red) Alpha Helix A PDB Code 1EEM Omega class glutathione transferase from homo sapiens

  5. Shared Mechanism of Dimer Interface Formation Throughout Many GST Classes Phi class (1BYE) Nu class (3GX0) Beta class (1N2A) Alpha class - MAII (1VF1) Omega class (1EEM) Zeta class - MAII (1FW1)

  6. Mechanism of Dimer Interface Formation in “Traditional” GST classes Alpha 2 Alpha helical domain A B C D Beta 3 Beta 4 Alpha 3 Alpha 1 Beta 1 Beta 2 N C N-terminal thioredoxin domain

  7. Subunit 1 (green/lemon) : Subunit 2 (teal,blue) Alpha 2 A B C D Beta 3 All Alpha Helical Domain Beta 4 Alpha 3 Alpha 1 Beta 1 Beta 2 C N Formation of the dimer interface C-terminal loop Loop from Alpha Helix C-D C-terminal loop YqjG – Glutathione Transferase from Escherichia coli

  8. Subunit 1 (lemon/orange) : Subunit 2 (magenta/pink) Alpha 2 A B C D N Beta 3 All Alpha Helical Domain Beta 4 Alpha 3 Alpha 1 Formation of the dimer interface Beta 1 Beta 2 C-terminal loop C N Loop from Alpha Helix C-D C-terminal loop PDB Code 3M1G The structure of a putative glutathione S-transferase from Corynebacteriumglutamicum Midwest Center for Structural Genomics, unpublished

  9. Structural superposition of YqjG (colored) and 3M1G (grey)

  10. Sequence Conservation Map 90° Identical Conserved Semi-conserved

  11. Electrostatic Surface Map 90°

  12. Sequence Conservation Map Electrostatic Surface Map K158 E204 D160 K161 R163 +//-/+- - YQJG_ECOLI VYKAGFATSQEAYDEAVAKVFESLARLEQILGQHRYLTGNQLTEADIRLWTTLVRFDPVYVTHFKCDKHRISDY Q8NR03_CORGL VYRTGFAGSQEAHNEAYKRLWVALDWLEDRLSTRRYLMGDHITEADIRLYPTLVRFDAVYHGHFKCGRNKITEM **::*** ****::** ::: :* **: *. :*** *:::*******:.******.** ****.:::*:: / / // // YQJG_ECOLI LNLYGFLRDIYQMPGIAETVNFDHIRNHYFRSHKTINPTGIISIGP-WQDLDEPHGRDVRFG-------------- Q8NR03_CORGL PNLWGYLRDLFQTPGFGDTTDFTEIKQHYYITHAEINPTRIVPVGPDLSGFATPHGREKLGGSPFAEGVTLPGPIP **:*:***::* **:.:*.:* .*::**: :* **** *:.:** ..: ****: *

  13. A New “Lock and Key” Motif PDB Code 1EEM Omega class glutathione transferase. PDB Code 1XW6 Mu class glutathione transferase. • GST Classes Alpha/Mu/Phi/Omega • Hydrophobic interface • “Lock and Key” mechanism

  14. A New “Lock and Key” Motif: YqjG

  15. CLUSTAL 2.0.12 multiple sequence alignment sp|P42620|YQJG_ECOLI MGQLIDGVWHDTWYDTKSTGGKFQRSASAFRNWLTADGAPG------PTG 44 tr|Q8NR03|Q8NR03_CORGL MANTSS-DWAGAPQN-ASADGEFVRDTNYIDDRIVADVPAGSEPIAQEDG 48 *.: . * .: : *:.*:* *.:. : : :.** ..* * --β1-- -----α1------ -β2- sp|P42620|YQJG_ECOLI TGGFIAEKDRYHLYVSLACPWAHRTLIMRKLKGLEPFISVSVVNPLMLEN 94 tr|Q8NR03|Q8NR03_CORGL TFHWPVEAGRYRLVAARACPWAHRTVITRRLLGLENVISLGLTGPTHDVR 98 * : .* .**:* .: ********:* *:* *** .**:.:..* . ------α2------ -β3- -β4 sp|P42620|YQJG_ECOLI GWTFDDSFPGATGDTLYQNEFLYQLYLHADPHYSGRVTVPVLWDKKNHTI 144 tr|Q8NR03|Q8NR03_CORGL SWTFD--LDPNHLDPVLQIPRLQDAYFNRFPDYPRGITVPALVEESSKKV 146 .**** : *.: * * : *:: *.*. :***.* ::..:.: -- -----α3-------- ---------αA------- sp|P42620|YQJG_ECOLI VSNESAEIIRMFNTAFDALG-AKAGDYYPPALQTKIDELNGWIYDTVNNG 193 tr|Q8NR03|Q8NR03_CORGL VTNDYPSITIDFNLEWKQFHREGAPNLYPAELREEMAPVMKRIFTEVNNG 196 *:*: ..* ** :. : * : **. *: :: : *: **** ------ --K-------αB----------- -----αC- sp|P42620|YQJG_ECOLI VYKAGFATSQEAYDEAVAKVFESLARLEQILGQHRYLTGNQLTEADIRLW 243 tr|Q8NR03|Q8NR03_CORGL VYRTGFAGSQEAHNEAYKRLWVALDWLEDRLSTRRYLMGDHITEADIRLY 246 **::*** ****::** ::: :* **: *. :*** *:::*******: ------- -----αD------ sp|P42620|YQJG_ECOLI TTLVRFDPVYVTHFKCDKHRISDYLNLYGFLRDIYQMPGIAETVNFDHIR 293 tr|Q8NR03|Q8NR03_CORGL PTLVRFDAVYHGHFKCGRNKITEMPNLWGYLRDLFQTPGFGDTTDFTEIK 296 .******.** ****.:::*:: **:*:***::* **:.:*.:* .*: LL sp|P42620|YQJG_ECOLI NHYFRSHKTINPTGIISIGP-WQDLDEPHGRDVRFG-------------- 328 tr|Q8NR03|Q8NR03_CORGL QHYYITHAEINPTRIVPVGPDLSGFATPHGREKLGGSPFAEGVTLPGPIP 346 :**: :* **** *:.:** ..: ****: * sp|P42620|YQJG_ECOLI ------------- tr|Q8NR03|Q8NR03_CORGL AGEEVKNPEPFQK 359 GSH Binding Dimer Interface Lock & Key

  16. Preliminary bioinformatics analysis and some questions YqjG and related sequences form a unique cluster. - What about the sequences in the YqjG cluster make them different/distinct from all other glutathione transferases. There are two structures from this subset of sequences that have this new, unique dimer interface. - Will all sequences in this cluster have the same dimer interface? - What is the sequence conservation at the dimer interface in this subset of sequences? - How does this set of sequences differ from other GST classes at the dimer interface? 3M1G and YqjG separate from each other around e-75 butwe know they have the same dimer interface, what is making them separate at these e-values.

  17. YqjG – Escherichia coli 3M1G – Corynebacteriumglutamicum PcpF – Sphingobiumchlorophenolicum 1e-14 1e-50 1e-75 1e-100

  18. YqjG – Escherichia coli 3M1G – Corynebacteriumglutamicum PcpF – Sphingobiumchlorophenolicum 1e-50 1e-80 1e-100 1e-125

  19. Multiple sequence alignment of 95 sequences in the YqjG ‘cluster’ +//-/+- - YQJG_ECOLI VYKAGFATSQEAYDEAVAKVFESLARLEQILGQHRYLTGNQLTEADIRLWTTLVRFDPVYVTHFKCDKHRISDY Q8NR03_CORGL VYRTGFAGSQEAHNEAYKRLWVALDWLEDRLSTRRYLMGDHITEADIRLYPTLVRFDAVYHGHFKCGRNKITEM **::*** ****::** ::: :* **: *. :*** *:::*******:.******.** ****.:::*:: / / // // YQJG_ECOLI LNLYGFLRDIYQMPGIAETVNFDHIRNHYFRSHKTINPTGIISIGP-WQDLDEPHGRDVRFG-------------- Q8NR03_CORGL PNLWGYLRDLFQTPGFGDTTDFTEIKQHYYITHAEINPTRIVPVGPDLSGFATPHGREKLGGSPFAEGVTLPGPIP **:*:***::* **:.:*.:* .*::**: :* **** *:.:** ..: ****: *

  20. Multiple sequence alignment 95 sequences 68 sequences

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