Modomics - A Database of RNA Modifications

ID Card:

Full name: RNA cap gamma-methyltransferase
Synonym: 7SK snRNA methylphosphate capping enzyme (MePCE), Bicoid-interacting protein 3 homolog
GI: 74758999
Orf: BCDIN3
COG: COG2264
UniProt: Q7L2J0
Structures: | 5UNA | 6DCB | 6DCC |
Alpha Fold Predicted Structure: AF-Q7L2J0-F1
Enzyme type: methyltransferase
Position of modification - modification: n:0 - m7GpppN


PDB Structures:


5UNA

Structure Description:

Title: Fragment of 7SK snRNA methylphosphate capping enzyme
Classification: TRANSFERASE
Technique: X-Ray Diffraction
Resolution: 2.55
R value free: 0.217
R value observed: 0.204
R value work: 0.204

Abstract of the PDB Structure's related Publication:

Among RNA 5'-cap structures, γ-phosphate monomethylation is unique to a small subset of noncoding RNAs, 7SK and U6 in humans. 7SK is capped by methylphosphate capping enzyme (MePCE), which has a second nonenzymatic role as a core component of the 7SK ribonuclear protein (RNP), an essential regulator of RNA transcription. We report 2.0- and 2.1-Å X-ray crystal structures of the human MePCE methyltransferase domain bound to S-adenosylhomocysteine (SAH) and uncapped or capped 7SK substrates, respectively. 7SK recognition is achieved by protein contacts to a 5'-hairpin-single-stranded RNA region, thus explaining MePCE's specificity for 7SK and U6. The structures reveal SAH and product RNA in a near-transition-state geometry. Unexpectedly, binding experiments showed that MePCE has higher affinity for capped versus uncapped 7SK, and kinetic data support a model of slow product release. This work reveals the molecular mechanism of methyl transfer and 7SK retention by MePCE for subsequent assembly of 7SK RNP.

Download RCSB-PDB Structures:

Pdb Files   5UNA.pdb   6DCB.pdb   6DCC.pdb  
Pdbx/mmCIF Files   5UNA.cif   6DCB.cif   6DCC.cif  


Protein sequence:

MIEMAAEKEPFLVPAPPPPLKDESGGGGGPTVPPHQEAASGELRGGTERGPGRCAPSAGSPAAAVGRESPGAAATSSSGPQAQQHRGGGPQAQSHGEARLSDPPGRAAPPDVGEERRGGGGTELGPPAPPRPRNGYQPHRPPGGGGGKRRNSCNVGGGGGGFKHPAFKRRRRVNSDCDSVLPSNFLLGGNIFDPLNLNSLLDEEVSRTLNAETPKSSPLPAKGRDPVEILIPKDITDPLSLNTCTDEGHVVLASPLKTGRKRHRHRGQHHQQQQAAGGSESHPVPPTAPLTPLLHGEGASQQPRHRGQNRDAPQPYELNTAINCRDEVVSPLPSALQGPSGSLSAPPAASVISAPPSSSSRHRKRRRTSSKSEAGARGGGQGSKEKGRGSWGGRHHHHHPLPAAGFKKQQRKFQYGNYCKYYGYRNPSCEDGRLRVLKPEWFRGRDVLDLGCNVGHLTLSIACKWGPSRMVGLDIDSRLIHSARQNIRHYLSEELRLPPQTLEGDPGAEGEEGTTTVRKRSCFPASLTASRGPIAAPQVPLDGADTSVFPNNVVFVTGNYVLDRDDLVEAQTPEYDVVLCLSLTKWVHLNWGDEGLKRMFRRIYRHLRPGGILVLEPQPWSSYGKRKTLTETIYKNYYRIQLKPEQFSSYLTSPDVGFSSYELVATPHNTSKGFQRPVYLFHKARSPSH

Comments:

7SK snRNA methyl phosphate capping enzyme belongs to the S-adenosyl-L-methionine-dependent methyltransferase enzyme family (SMA). Specifically, BCDIN3 ads a methyl phosphate at the 5'-end of the 7SK snRNA (7SKRNA), stabilizing it (Xue et al. 2010 ; Jeronimo et al. 2007 ).

Noteworthy, it also has a non-enzymatic function as part of the 7SK RNP complex, sequestering the positive transcription elongation factor b(P-TEFb) in large inactive 7SK RNP complex preventing RNA polymerase II phosphorylation nd subsequent transcriptional elongation (Xue et al. 2010 ; Jeronimo et al. 2007 ).





Alpha Fold Predicted Structure:




Downloading... [556794/599026]


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Protein sequence:

M I E M A A E K E P F L V P A P P P P L K D E S G G G G G P T V P P H Q E A A S G E L R G G T E R G P G R C A P S A G S P A A A V G R E S P G A A A T S S S G P Q A Q Q H R G G G P Q A Q S H G E A R L S D P P G R A A P P D V G E E R R G G G G T E L G P P A P P R P R N G Y Q P H R P P G G G G G K R R N S C N V G G G G G G F K H P A F K R R R R V N S D C D S V L P S N F L L G G N I F D P L N L N S L L D E E V S R T L N A E T P K S S P L P A K G R D P V E I L I P K D I T D P L S L N T C T D E G H V V L A S P L K T G R K R H R H R G Q H H Q Q Q Q A A G G S E S H P V P P T A P L T P L L H G E G A S Q Q P R H R G Q N R D A P Q P Y E L N T A I N C R D E V V S P L P S A L Q G P S G S L S A P P A A S V I S A P P S S S S R H R K R R R T S S K S E A G A R G G G Q G S K E K G R G S W G G R H H H H H P L P A A G F K K Q Q R K F Q Y G N Y C K Y Y G Y R N P S C E D G R L R V L K P E W F R G R D V L D L G C N V G H L T L S I A C K W G P S R M V G L D I D S R L I H S A R Q N I R H Y L S E E L R L P P Q T L E G D P G A E G E E G T T T V R K R S C F P A S L T A S R G P I A A P Q V P L D G A D T S V F P N N V V F V T G N Y V L D R D D L V E A Q T P E Y D V V L C L S L T K W V H L N W G D E G L K R M F R R I Y R H L R P G G I L V L E P Q P W S S Y G K R K T L T E T I Y K N Y Y R I Q L K P E Q F S S Y L T S P D V G F S S Y E L V A T P H N T S K G F Q R P V Y L F H K A R S P S H
100200300400500600SequenceGHTBSN

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-Q7L2J0-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q7L2J0-F1.cif  
DSSP Secondary Structures   Q7L2J0.dssp  





Publications: