TOPSAN > Proteins > JCSG > 3e11

3e11

Page last modified 23:22, 20 May 2009 by dweekes

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Summary Discussions

1. Protein Summary
2. Ligand Summary

Molecular Characteristics
Title	Crystal structure of predicted zincin-like metalloprotease (YP_873820.1) from ACIDOTHERMUS CELLULOLYTICUS 11B at 1.80 A resolution.
Site	JCSG
PDB Id	3e11	Target Id	376525
Source	Acidothermus cellulolyticus 11b
Alias Ids	YP_873820.1	Molecular Weight	12831.74 Da.
Residues	113	Isoelectric Point	4.29
Sequence	mvyvdpdrfdelvaealdgipeefaramrnvavfvedepddpellglyvgiplterttayggvlpdriii yrnticalcetesevidevrktvvheiahhfgidderlhelgy
	BLAST FFAS

Structure Determination
Method	XRAY	Chains	2
Resolution (Å)	1.80	Rfree	0.204
Matthews' coefficent	2.07	Rfactor	0.175
Waters	193	Solvent Content	40.54

Ligand Information
Ligands	ACT (ACETATE) x 2
Metals	CA (CALCIUM) x 2

Jmol

Resources
- PDB
- PDBSum
- PSI-KB
- PlasmID
- Proteopedia
- GPSS
- ProFunc

Protein Summary

Structure of YP_873820.1 protein represents the second experimentally determined structure from PFAM DUF1025 family (PF06262), a large (>200 members) family of hypothetical proteins from bacteria and human, soil and ocean metagenomes. The first structure from this family (2ejq from Thermus thermophilus HB8) was solved by Riken Structural Genomics group in 2007. Both structures have significant stuctural similarity to metalloproteases such as MMP16 (1rn8) and others from Peptidase MA clan. Depite the low sequence identity (~8% sequence id), the classical MMP motif (HEXXHXXGXXH) is conserved in this family except for the last histidine. At the same time distant homology prediction programs recognize this similarity, even that with a marginal statistical significance (FFAS Z-score of -8.9 as compared to -9.5 significance treshold), suggesting that DUF1025 family is distantly related to metalloproteases and should be added to the Peptidase MA clan.

Structures of both representatives of DUF1025 family look like minimal versions of the metalloprotease fold, only three (out of 5) stands in the main beta sheet are conserved, loops are much closer and the overall length of all members of this family (~110 aa) is significantly shorter that the average MMP (~160aa)