8JT1

COLLAGENASE FROM GRIMONTIA (VIBRIO) HOLLISAE 1706B COMPLEXED WITH GLY-PRO-HYP-GLY-PRO-HYP

PDB DOI: https://doi.org/10.2210/pdb8JT1/pdb

Classification: HYDROLASE
Organism(s): Grimontia hollisae, synthetic construct
Expression System: Brevibacillus
Mutation(s): No

Deposited: 2023-06-21 Released: 2024-02-07
Deposition Author(s): Ueshima, S., Yaskawa, K., Takita, T., Mikami, B.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.214
R-Value Work: 0.176
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Insights into the catalytic mechanism of Grimontia hollisae collagenase through structural and mutational analyses.

Ueshima, S., Yasumoto, M., Kitagawa, Y., Akazawa, K., Takita, T., Tanaka, K., Hattori, S., Mizutani, K., Mikami, B., Yasukawa, K.

(2023) FEBS Lett 597: 2473-2483

PubMed: 37698340 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.14732
Primary Citation of Related Structures:
8JT1

PubMed Abstract:
Grimontia hollisae collagenase (Ghcol) exhibits high collagen-degrading activity. To explore its catalytic mechanism, its substrate (Gly-Pro-Hyp-Gly-Pro-Hyp, GPOGPO)-complexed crystal structure was determined at 2.0 Å resolution. A water molecule was observed near the active-site zinc ion. Since this water was not observed in the product (GPO)-complexed Ghcol, it was hypothesized that the GPOGPO-complexed Ghcol structure reflects a Michaelis complex, providing a structural basis for understanding the catalytic mechanism. Analyses of the active-site geometry and site-directed mutagenesis of the active-site tyrosine residues revealed that Glu493 and Tyr564 were essential for catalysis, suggesting that Glu493 functions as an acid and base catalyst while Tyr564 stabilizes the tetrahedral complex in the transition state. These results shed light on the catalytic mechanism of bacterial collagenase.

Organizational Affiliation

Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Japan.

Macromolecule Content

Total Structure Weight: 133.47 kDa
Atom Count: 9,660
Modelled Residue Count: 1,094
Deposited Residue Count: 1,154
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microbial collagenase	A, B	559	Grimontia hollisae	Mutation(s): 0 EC: 3.4.24.3
UniProt
Find proteins for F7IZI6 (Grimontia hollisae) Explore F7IZI6 Go to UniProtKB: F7IZI6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F7IZI6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
6-mer peptide	C D [auth E] E [auth F] F [auth G] G [auth I] C, D [auth E], E [auth F], F [auth G], G [auth I], H [auth J]	6	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE (Subject of Investigation/LOI) Query on PGE Download Ideal Coordinates CCD File SDF format, chain FB [auth A] MOL2 format, chain FB [auth A]	FB [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain FB [auth A] Interactions & Density Focus chain FB [auth A]
TRS (Subject of Investigation/LOI) Query on TRS Download Ideal Coordinates CCD File SDF format, chain FD [auth B] MOL2 format, chain FD [auth B]	FD [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain FD [auth B] Interactions & Density Focus chain FD [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain ED [auth B] MOL2 format, chain ED [auth B]	ED [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain ED [auth B] Interactions & Density Focus chain ED [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain GB [auth B] SDF format, chain I [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain I [auth A]	GB [auth B], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain GB [auth B] Focus chain I [auth A] Interactions & Density Focus chain GB [auth B] Focus chain I [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth A] SDF format, chain AC [auth B] SDF format, chain AD [auth B] SDF format, chain BA [auth A] SDF format, chain BB [auth A] SDF format, chain BC [auth B] SDF format, chain BD [auth B] SDF format, chain CA [auth A] SDF format, chain CB [auth A] SDF format, chain CC [auth B] SDF format, chain CD [auth B] SDF format, chain DA [auth A] SDF format, chain DB [auth A] SDF format, chain DC [auth B] SDF format, chain DD [auth B] SDF format, chain EA [auth A] SDF format, chain EB [auth A] SDF format, chain EC [auth B] SDF format, chain FA [auth A] SDF format, chain FC [auth B] SDF format, chain GA [auth A] SDF format, chain GC [auth B] SDF format, chain HA [auth A] SDF format, chain HC [auth B] SDF format, chain IA [auth A] SDF format, chain IC [auth B] SDF format, chain JA [auth A] SDF format, chain JC [auth B] SDF format, chain KA [auth A] SDF format, chain KC [auth B] SDF format, chain LA [auth A] SDF format, chain LB [auth B] SDF format, chain LC [auth B] SDF format, chain MA [auth A] SDF format, chain MB [auth B] SDF format, chain MC [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth A] SDF format, chain NB [auth B] SDF format, chain NC [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth A] SDF format, chain OB [auth B] SDF format, chain OC [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth A] SDF format, chain PB [auth B] SDF format, chain PC [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth A] SDF format, chain QB [auth B] SDF format, chain QC [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth A] SDF format, chain RB [auth B] SDF format, chain RC [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth A] SDF format, chain SB [auth B] SDF format, chain SC [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth A] SDF format, chain TB [auth B] SDF format, chain TC [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth A] SDF format, chain UB [auth B] SDF format, chain UC [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth A] SDF format, chain VB [auth B] SDF format, chain VC [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth A] SDF format, chain WB [auth B] SDF format, chain WC [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth A] SDF format, chain XB [auth B] SDF format, chain XC [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth A] SDF format, chain YB [auth B] SDF format, chain YC [auth B] SDF format, chain Z [auth A] SDF format, chain ZA [auth A] SDF format, chain ZB [auth B] SDF format, chain ZC [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain AC [auth B] MOL2 format, chain AD [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain BC [auth B] MOL2 format, chain BD [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth A] MOL2 format, chain CC [auth B] MOL2 format, chain CD [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth A] MOL2 format, chain DC [auth B] MOL2 format, chain DD [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth A] MOL2 format, chain EC [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain FC [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain GC [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain HC [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain IC [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain JC [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain KC [auth B] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth B] MOL2 format, chain LC [auth B] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth B] MOL2 format, chain MC [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth B] MOL2 format, chain NC [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth B] MOL2 format, chain OC [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth B] MOL2 format, chain PC [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth B] MOL2 format, chain QC [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain RB [auth B] MOL2 format, chain RC [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth B] MOL2 format, chain SC [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth B] MOL2 format, chain TC [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain UB [auth B] MOL2 format, chain UC [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain VB [auth B] MOL2 format, chain VC [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain WB [auth B] MOL2 format, chain WC [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain XB [auth B] MOL2 format, chain XC [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain YB [auth B] MOL2 format, chain YC [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth A] MOL2 format, chain ZB [auth B] MOL2 format, chain ZC [auth B]	AA [auth A] AB [auth A] AC [auth B] AD [auth B] BA [auth A] AA [auth A], AB [auth A], AC [auth B], AD [auth B], BA [auth A], BB [auth A], BC [auth B], BD [auth B], CA [auth A], CB [auth A], CC [auth B], CD [auth B], DA [auth A], DB [auth A], DC [auth B], DD [auth B], EA [auth A], EB [auth A], EC [auth B], FA [auth A], FC [auth B], GA [auth A], GC [auth B], HA [auth A], HC [auth B], IA [auth A], IC [auth B], JA [auth A], JC [auth B], KA [auth A], KC [auth B], LA [auth A], LB [auth B], LC [auth B], MA [auth A], MB [auth B], MC [auth B], N [auth A], NA [auth A], NB [auth B], NC [auth B], O [auth A], OA [auth A], OB [auth B], OC [auth B], P [auth A], PA [auth A], PB [auth B], PC [auth B], Q [auth A], QA [auth A], QB [auth B], QC [auth B], R [auth A], RA [auth A], RB [auth B], RC [auth B], S [auth A], SA [auth A], SB [auth B], SC [auth B], T [auth A], TA [auth A], TB [auth B], TC [auth B], U [auth A], UA [auth A], UB [auth B], UC [auth B], V [auth A], VA [auth A], VB [auth B], VC [auth B], W [auth A], WA [auth A], WB [auth B], WC [auth B], X [auth A], XA [auth A], XB [auth B], XC [auth B], Y [auth A], YA [auth A], YB [auth B], YC [auth B], Z [auth A], ZA [auth A], ZB [auth B], ZC [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth A] Focus chain AC [auth B] Focus chain AD [auth B] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain BC [auth B] Focus chain BD [auth B] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain CC [auth B] Focus chain CD [auth B] Focus chain DA [auth A] Focus chain DB [auth A] Focus chain DC [auth B] Focus chain DD [auth B] Focus chain EA [auth A] Focus chain EB [auth A] Focus chain EC [auth B] Focus chain FA [auth A] Focus chain FC [auth B] Focus chain GA [auth A] Focus chain GC [auth B] Focus chain HA [auth A] Focus chain HC [auth B] Focus chain IA [auth A] Focus chain IC [auth B] Focus chain JA [auth A] Focus chain JC [auth B] Focus chain KA [auth A] Focus chain KC [auth B] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain LC [auth B] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain MC [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain NB [auth B] Focus chain NC [auth B] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain OC [auth B] Focus chain P [auth A] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain PC [auth B] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain QC [auth B] Focus chain R [auth A] Focus chain RA [auth A] Focus chain RB [auth B] Focus chain RC [auth B] Focus chain S [auth A] Focus chain SA [auth A] Focus chain SB [auth B] Focus chain SC [auth B] Focus chain T [auth A] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain TC [auth B] Focus chain U [auth A] Focus chain UA [auth A] Focus chain UB [auth B] Focus chain UC [auth B] Focus chain V [auth A] Focus chain VA [auth A] Focus chain VB [auth B] Focus chain VC [auth B] Focus chain W [auth A] Focus chain WA [auth A] Focus chain WB [auth B] Focus chain WC [auth B] Focus chain X [auth A] Focus chain XA [auth A] Focus chain XB [auth B] Focus chain XC [auth B] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain YB [auth B] Focus chain YC [auth B] Focus chain Z [auth A] Focus chain ZA [auth A] Focus chain ZB [auth B] Focus chain ZC [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth A] Focus chain AC [auth B] Focus chain AD [auth B] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain BC [auth B] Focus chain BD [auth B] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain CC [auth B] Focus chain CD [auth B] Focus chain DA [auth A] Focus chain DB [auth A] Focus chain DC [auth B] Focus chain DD [auth B] Focus chain EA [auth A] Focus chain EB [auth A] Focus chain EC [auth B] Focus chain FA [auth A] Focus chain FC [auth B] Focus chain GA [auth A] Focus chain GC [auth B] Focus chain HA [auth A] Focus chain HC [auth B] Focus chain IA [auth A] Focus chain IC [auth B] Focus chain JA [auth A] Focus chain JC [auth B] Focus chain KA [auth A] Focus chain KC [auth B] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain LC [auth B] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain MC [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain NB [auth B] Focus chain NC [auth B] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain OC [auth B] Focus chain P [auth A] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain PC [auth B] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain QC [auth B] Focus chain R [auth A] Focus chain RA [auth A] Focus chain RB [auth B] Focus chain RC [auth B] Focus chain S [auth A] Focus chain SA [auth A] Focus chain SB [auth B] Focus chain SC [auth B] Focus chain T [auth A] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain TC [auth B] Focus chain U [auth A] Focus chain UA [auth A] Focus chain UB [auth B] Focus chain UC [auth B] Focus chain V [auth A] Focus chain VA [auth A] Focus chain VB [auth B] Focus chain VC [auth B] Focus chain W [auth A] Focus chain WA [auth A] Focus chain WB [auth B] Focus chain WC [auth B] Focus chain X [auth A] Focus chain XA [auth A] Focus chain XB [auth B] Focus chain XC [auth B] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain YB [auth B] Focus chain YC [auth B] Focus chain Z [auth A] Focus chain ZA [auth A] Focus chain ZB [auth B] Focus chain ZC [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain HB [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KB [auth B] SDF format, chain M [auth A] SDF format, chain IB [auth B] SDF format, chain JB [auth B] SDF format, chain L [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain M [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain JB [auth B] MOL2 format, chain L [auth A]	HB [auth B] IB [auth B] J [auth A] JB [auth B] K [auth A] HB [auth B], IB [auth B], J [auth A], JB [auth B], K [auth A], KB [auth B], L [auth A], M [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain HB [auth B] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain HB [auth B] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain M [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP Query on HYP	C D [auth E] E [auth F] F [auth G] G [auth I] C, D [auth E], E [auth F], F [auth G], G [auth I], H [auth J]	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO