Database accession: MF3120002
Name: DUF16 domain of MPN010 (Mycoplasma pneumoniae)
PDB ID: 2ba2
Experimental method: X-ray (1.80 Å)
Assembly: Homotrimer
Source organism: Mycoplasma pneumoniae
Primary publication of the structure:
Shin DH, Kim JS, Yokota H, Kim R, Kim SH
Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae.
(2006) Protein Sci. 15: 921-8
PMID: 16522803
Abstract:
We have determined the crystal structure of the DUF16 domain of unknown function encoded by the gene MPN010 of Mycoplasma pneumoniae at 1.8 A resolution. The crystal structure revealed that this domain is composed of two separated homotrimeric coiled-coils. The shorter one consists of 11 highly conserved residues. The sequence comprises noncanonical heptad repeats that induce a right-handed coiled-coil structure. The longer one is composed of approximately nine heptad repeats. In this coiled-coil structure, there are three distinguishable regions that confer unique structural properties compared with other known homotrimeric coiled-coils. The first part, containing one stutter, is an unusual phenylalanine-rich region that is not found in any other coiled-coil structures. The second part is a highly conserved glutamine-rich region, frequently found in other trimeric coiled-coil structures. The last part is composed of prototype heptad repeats. The phylogenetic analysis of the DUF16 family together with a secondary structure prediction shows that the DUF16 family can be classified into five subclasses according to N-terminal sequences. Based on the structural comparison with other coiled-coil structures, a probable molecular function of the DUF16 family is discussed.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.Molecular function: not assigned
Biological process: not assigned
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 3 distinct polypeptide molecules
Chains: A, B, C
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: UPF0134 protein MPN_010
Source organism: Mycoplasma pneumoniae
Length: 131 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAYSPSLNDIKSILNKYTSKDYELKCENRYDGKLELWLKGVFEEIVKTPGTRYVTHKQLDEKLKNFVTKTEFKEFQTVVMESFAVQNQNIDAQGEQIKELQVEQKAQGKTLQLILEALQGINKRLDNLESK
UniProtKB AC: P75103 (positions: 50-130)
Coverage: 61%
Name: UPF0134 protein MPN_010
Source organism: Mycoplasma pneumoniae
Length: 131 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAYSPSLNDIKSILNKYTSKDYELKCENRYDGKLELWLKGVFEEIVKTPGTRYVTHKQLDEKLKNFVTKTEFKEFQTVVMESFAVQNQNIDAQGEQIKELQVEQKAQGKTLQLILEALQGINKRLDNLESK
UniProtKB AC: P75103 (positions: 51-130)
Coverage: 61%
Name: UPF0134 protein MPN_010
Source organism: Mycoplasma pneumoniae
Length: 131 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAYSPSLNDIKSILNKYTSKDYELKCENRYDGKLELWLKGVFEEIVKTPGTRYVTHKQLDEKLKNFVTKTEFKEFQTVVMESFAVQNQNIDAQGEQIKELQVEQKAQGKTLQLILEALQGINKRLDNLESK
UniProtKB AC: P75103 (positions: 50-130)
Coverage: 61%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: -
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
The subunits in the structure are bound via coiled coil interactions (PMID:16522803). Coiled coils are highly versatile folding units (PMID:11166216), where the formation of the structure and the interaction between subunits is almost ubiquitously linked. This cooperative nature of binding and folding that results in a two-step process has been demonstrated for coiled coils with varying oligomeric state from dimers (PMID:9811815) and trimers (PMID:10933510) up to heptamers (PMID:17030805). While the interaction and folding are linked, in certain cases there can be significant residual structure before association (PMID:8401212). However, these residual structural elements usually encompass 1-2 turns of helices that serve as a 'nucleation site' driving interaction and helix formation (zipping up) (PMID:17438295), thus even in these cases monomeric coiled coil subunits cannot be considered to have a stable structure.
Chain A:
N/A
Chain B:
N/A
Chain C:
N/A
Surface and contacts features:
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). No related structure was found in the MFIB database.
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