7UQW

PCC6803 Cyanophycinase S132DAP covalently bound to cyanophycin dimer

PDB DOI: https://doi.org/10.2210/pdb7UQW/pdb

Classification: HYDROLASE
Organism(s): Synechocystis sp. PCC 6803
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-04-20 Released: 2022-08-10
Deposition Author(s): Sharon, I., Schmeing, T.M.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.199
R-Value Work: 0.181
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The structure of cyanophycinase in complex with a cyanophycin degradation intermediate.

Sharon, I., Grogg, M., Hilvert, D., Schmeing, T.M.

(2022) Biochim Biophys Acta Gen Subj 1866: 130217-130217

PubMed: 35905922 Search on PubMed
DOI: https://doi.org/10.1016/j.bbagen.2022.130217
Primary Citation of Related Structures:
7UQV, 7UQW

PubMed Abstract:
Cyanophycinases are serine protease family enzymes which are required for the metabolism of cyanophycin, the natural polymer multi-L-arginyl-poly(L-aspartic acid). Cyanophycinases degrade cyanophycin to β-Asp-Arg dipeptides, which enables use of this important store of fixed nitrogen.

Organizational Affiliation

Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada.

Macromolecule Content

Total Structure Weight: 92.5 kDa
Atom Count: 6,657
Modelled Residue Count: 792
Deposited Residue Count: 828
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyanophycinase	A, B, C	276	Synechocystis sp. PCC 6803	Mutation(s): 1 Gene Names: cphB, slr2001 EC: 3.4.15.6
UniProt
Find proteins for P73832 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P73832 Go to UniProtKB: P73832
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P73832
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7ID (Subject of Investigation/LOI) Query on 7ID Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C]	D [auth A] E [auth A] G [auth B] H [auth B] N [auth C] D [auth A], E [auth A], G [auth B], H [auth B], N [auth C], O [auth C]	(2~{S})-4-[[(2~{S})-5-[[azanyl($l^{4}-azanylidene)methyl]amino]-1-$l^{1}-oxidanyl-1-oxidanylidene-pentan-2-yl]amino]-2-$l^{2}-azanyl-4-oxidanylidene-butanoic acid C₁₀ H₁₉ N₅ O₅ QCGCETFHYOEVAI-WDSKDSINSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain N [auth C] Focus chain O [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ARF Query on ARF Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C]	I [auth B] J [auth B] K [auth B] L [auth B] M [auth B] I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], P [auth C], Q [auth C]	FORMAMIDE C H₃ N O ZHNUHDYFZUAESO-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C]