Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
Synonym: GidA
GI: 21675089
COG: COG0445
UniProt: Q8KA85
Structures: | 3CP8 |
Alpha Fold Predicted Structure: AF-Q8KA85-F1
Complex: MnmG/MnmE
Enzyme type: other
Position of modification - modification: t:34 - cmnm5s2U
t:34 - cmnm5U


PDB Structures:


3CP8

Structure Description:

Title: Crystal structure of GidA from Chlorobium tepidum
Classification: OXIDOREDUCTASE
Technique: X-Ray Diffraction
Resolution: 3.2
R value free: 0.278
R value observed: 0.256
R value work: 0.254

Abstract of the PDB Structure's related Publication:

GidA is a flavin-adenine-dinucleotide (FAD)-binding protein that is conserved among bacteria and eucarya. Together with MnmE, it is involved in the addition of a carboxymethylaminomethyl group to the uridine base in the wobble position (nucleotide 34) of tRNAs that read split codon boxes. Here, we report the crystal structures of the GidA proteins from both Escherichia coli and Chlorobium tepidum. The structures show that the protein can be divided into three domains: a first FAD-binding domain showing the classical Rossmann fold, a second alpha/beta domain inserted between two strands of the Rossmann fold, and an alpha-helical C-terminal domain. The domain inserted into the Rossmann fold displays structural similarity to the nicotinamide-adenine-dinucleotide-(phosphate)-binding domains of phenol hydroxylase and 3-hydroxy-3-methylglutaryl-CoA reductase, and, correspondingly, we show that GidA binds NADH with high specificity as an initial donor of electrons. GidA behaves as a homodimer in solution. As revealed by the crystal structures, homodimerization is mediated via both the FAD-binding domain and the NADH-binding domain. Finally, a large patch of highly conserved, positively charged residues on the surface of GidA leading to the FAD-binding site suggests a tRNA-binding surface. We propose a model for the interaction between GidA and MnmE, which is supported by site-directed mutagenesis. Our data suggest that this interaction is modulated and potentially regulated by the switch function of the G domain of MnmE.

Download RCSB-PDB Structures:

Pdb Files   3CP8.pdb  
Pdbx/mmCIF Files   3CP8.cif  


Protein sequence:

MYDVIVVGAGHAGCEAALAVARGGLHCLLITSDLSAVARMSCNPAIGGVAKGQITREIDALGGEMGKAIDATGIQFRMLNRSKGPAMHSPRAQADKTQYSLYMRRIVEHEPNIDLLQDTVIGVSANSGKFSSVTVRSGRAIQAKAAILACGTFLNGLIHIGMDHFPGGRSTAEPPVEGLTESLASLGFSFGRLKTGTPPRIDSRSVDYTIVTEQPGDVDPVPFSFSSTSVANRNLVSCYLTKTTEKTHDILRTGFDRSPLFTGKVQGVGPRYCPSIEDKISRFPDKSSHHIFLEPEGTDTVEMYVNGFSTSLPEDIQIAGLRSIPGLEEAKMIRPGYAIEYDFFHPWQIRSTMETRPVENLFFAGQINGTSGYEEAAAQGLMAGINAVRKILGKELIVLGRDQAYIGVLIDDLITKETKEPYRMFTSSAEHRLILRHDNADLRLRKIGYDCNLVSSDDLHRTESIIKRVQHCLEVMKTAKVTPAEINTLLMNKGLQELKTPARALSLIKRPGISLQDILEHSLSVRSAAEELCNDPRVAEQVQIEIKYEGYIKREQLVADRIARLDSLHIPDNFNYDSLNSLSSEGREKLLKHRPATIGQASRILGVSPSDVSILMIRLGR

Comments:

Homologue of E. coli MnmG. Flavoprotein, using methyl-(or methylen)-tetrahydrofolate as a donor of one carbon. In a complex with GTPase MnmE they catalyze the formation of either cmnm5U or nm5U by reacting either with glycine or with ammonium.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M Y D V I V V G A G H A G C E A A L A V A R G G L H C L L I T S D L S A V A R M S C N P A I G G V A K G Q I T R E I D A L G G E M G K A I D A T G I Q F R M L N R S K G P A M H S P R A Q A D K T Q Y S L Y M R R I V E H E P N I D L L Q D T V I G V S A N S G K F S S V T V R S G R A I Q A K A A I L A C G T F L N G L I H I G M D H F P G G R S T A E P P V E G L T E S L A S L G F S F G R L K T G T P P R I D S R S V D Y T I V T E Q P G D V D P V P F S F S S T S V A N R N L V S C Y L T K T T E K T H D I L R T G F D R S P L F T G K V Q G V G P R Y C P S I E D K I S R F P D K S S H H I F L E P E G T D T V E M Y V N G F S T S L P E D I Q I A G L R S I P G L E E A K M I R P G Y A I E Y D F F H P W Q I R S T M E T R P V E N L F F A G Q I N G T S G Y E E A A A Q G L M A G I N A V R K I L G K E L I V L G R D Q A Y I G V L I D D L I T K E T K E P Y R M F T S S A E H R L I L R H D N A D L R L R K I G Y D C N L V S S D D L H R T E S I I K R V Q H C L E V M K T A K V T P A E I N T L L M N K G L Q E L K T P A R A L S L I K R P G I S L Q D I L E H S L S V R S A A E E L C N D P R V A E Q V Q I E I K Y E G Y I K R E Q L V A D R I A R L D S L H I P D N F N Y D S L N S L S S E G R E K L L K H R P A T I G Q A S R I L G V S P S D V S I L M I R L G R
50100150200250300350400450500550600SequenceGHTBSN

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-Q8KA85-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q8KA85-F1.cif  
DSSP Secondary Structures   Q8KA85.dssp  





Publications:

Links:

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