General Information

Database accession: MF7000823

Name: DcpS with m7GpppA

PDB ID: 1st4 PDBe

Experimental method: X-ray (2.02 Å)

Assembly: Homodimer

Source organism: Homo sapiens

Primary publication of the structure:

Gu M, Fabrega C, Liu SW, Liu H, Kiledjian M, Lima CD
Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity.
(2004) Mol. Cell 14: 67-80

PMID: 15068804 PubMed

Abstract:

Complete removal of residual N-7 guanine cap from degraded messenger RNA is necessary to prevent accumulation of intermediates that might interfere with RNA processing, export, and translation. The human scavenger decapping enzyme, DcpS, catalyzes residual cap hydrolysis following mRNA degradation, releasing N-7 methyl guanosine monophosphate and 5'-diphosphate terminated cap or mRNA products. DcpS structures bound to m(7)GpppG or m(7)GpppA reveal an asymmetric DcpS dimer that simultaneously creates an open nonproductive DcpS-cap complex and a closed productive DcpS-cap complex that alternate via 30 A domain movements. Structural and biochemical analysis suggests an autoregulatory mechanism whereby premature decapping mRNA is prevented by blocking the conformational changes that are required to form a closed productive active site capable of cap hydrolysis.


Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function:

5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity GeneOntology

identical protein binding identical protein binding GeneOntology

RNA 7-methylguanosine cap binding RNA 7-methylguanosine cap binding GeneOntology

RNA exonuclease activity RNA exonuclease activity GeneOntology

Biological process:

deadenylation-dependent decapping of nuclear-transcribed mRNA deadenylation-dependent decapping of nuclear-transcribed mRNA GeneOntology

mRNA cis splicing, via spliceosome mRNA cis splicing, via spliceosome GeneOntology

mRNA methylguanosine-cap decapping mRNA methylguanosine-cap decapping GeneOntology

nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay GeneOntology

Cellular component:

cytoplasm cytoplasm GeneOntology

cytosol cytosol GeneOntology

mitochondrion mitochondrion GeneOntology

nucleoplasm nucleoplasm GeneOntology

nucleus nucleus GeneOntology

P-body P-body GeneOntology

Structure Summary Structural annotations of the participating protein chains.

Entry contents: 2 distinct polypeptide molecules

Chains: A, B

Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.

Number of unique protein segments: 1


Chain A

Name: m7GpppX diphosphatase

Source organism: Homo sapiens

Length: 337 residues

Sequence:Sequence according to the corresponding UniProt protein segmentMADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS

UniProtKB AC: Q96C86 (positions: 38-337) UniProt

Coverage: 89%

Chain B

Name: m7GpppX diphosphatase

Source organism: Homo sapiens

Length: 337 residues

Sequence:Sequence according to the corresponding UniProt protein segmentMADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS

UniProtKB AC: Q96C86 (positions: 40-336) UniProt

Coverage: 88%

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

Representative domain in related structures: Scavenger mRNA decapping enzyme (DcpS)

Evidence level: Indirect evidence

Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.

Complex Evidence:

Multidomain structure, where the domain-swapped N-terminal domain is responsible for dimerization. The extensive interface, symmetry, topology, beta sheet augmentation and buried surface area suggest that the N-terminal dimerization domain behaves as a single rigid domain and the monomers would not be stable on their own. Gel-filtration chromatography also suggested a dimeric form (PMID:15068804).

Chain B:

N/A

Chain A:

N/A

Surface and contacts features:

Related Structure(s) Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap).

There are 8 related structures in the MFIB database:






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