8WT1

Crystal structure of S9 carboxypeptidase from Geobacillus sterothermophilus

PDB DOI: https://doi.org/10.2210/pdb8WT1/pdb

Classification: HYDROLASE
Organism(s): Geobacillus stearothermophilus ATCC 12980
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-17 Released: 2024-03-13
Deposition Author(s): Chandravanshi, K., Kumar, A., Sen, C., Singh, R., Bhange, G.B., Makde, R.D.
Funding Organization(s): Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.256
R-Value Work: 0.212
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure and solution scattering of Geobacillus stearothermophilus S9 peptidase reveal structural adaptations for carboxypeptidase activity.

Chandravanshi, K., Singh, R., Bhange, G.N., Kumar, A., Yadav, P., Kumar, A., Makde, R.D.

(2024) FEBS Lett 598: 684-701

PubMed: 38426217 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.14834
Primary Citation of Related Structures:
8WT1

PubMed Abstract:
Acylaminoacyl peptidases (AAPs) play a pivotal role in various pathological conditions and are recognized as potential therapeutic targets. AAPs exhibit a wide range of activities, such as acylated amino acid-dependent aminopeptidase, endopeptidase, and less studied carboxypeptidase activity. We have determined the crystal structure of an AAP from Geobacillus stearothermophilus (S9gs) at 2.0 Å resolution. Despite being annotated as an aminopeptidase in the NCBI database, our enzymatic characterization proved S9gs to be a carboxypeptidase. Solution-scattering studies showed that S9gs exists as a tetramer in solution, and crystal structure analysis revealed adaptations responsible for the carboxypeptidase activity of S9gs. The findings present a hypothesis for substrate selection, substrate entry, and product exit from the active site, enriching our understanding of this rare carboxypeptidase.

Organizational Affiliation

Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, India.

Macromolecule Content

Total Structure Weight: 627.53 kDa
Atom Count: 42,813
Modelled Residue Count: 5,197
Deposited Residue Count: 5,528
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S9 family peptidase	A, B, C, D, E A, B, C, D, E, F, G, H	691	Geobacillus stearothermophilus ATCC 12980	Mutation(s): 0 Gene Names: D9548_14720
UniProt
Find proteins for A0A3L7D5Q2 (Geobacillus stearothermophilus) Explore A0A3L7D5Q2 Go to UniProtKB: A0A3L7D5Q2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3L7D5Q2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC (Subject of Investigation/LOI) Query on FLC Download Ideal Coordinates CCD File SDF format, chain QD [auth H] SDF format, chain Y [auth A] MOL2 format, chain QD [auth H] MOL2 format, chain Y [auth A]	QD [auth H], Y [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain QD [auth H] Focus chain Y [auth A] Interactions & Density Focus chain QD [auth H] Focus chain Y [auth A]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AC [auth E] SDF format, chain BA [auth B] SDF format, chain BC [auth E] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain ED [auth H] SDF format, chain FA [auth B] SDF format, chain FB [auth D] SDF format, chain FD [auth H] SDF format, chain GA [auth B] SDF format, chain GB [auth D] SDF format, chain GD [auth H] SDF format, chain HA [auth B] SDF format, chain HB [auth D] SDF format, chain HD [auth H] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain IB [auth D] SDF format, chain IC [auth F] SDF format, chain ID [auth H] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain JB [auth D] SDF format, chain JC [auth F] SDF format, chain JD [auth H] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth D] SDF format, chain KC [auth F] SDF format, chain KD [auth H] SDF format, chain L [auth A] SDF format, chain LB [auth D] SDF format, chain LC [auth F] SDF format, chain LD [auth H] SDF format, chain M [auth A] SDF format, chain MB [auth D] SDF format, chain MC [auth F] SDF format, chain MD [auth H] SDF format, chain N [auth A] SDF format, chain NC [auth F] SDF format, chain O [auth A] SDF format, chain OC [auth F] SDF format, chain P [auth A] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain TB [auth E] SDF format, chain UA [auth C] SDF format, chain UB [auth E] SDF format, chain VA [auth C] SDF format, chain VB [auth E] SDF format, chain VC [auth G] SDF format, chain WA [auth C] SDF format, chain WB [auth E] SDF format, chain WC [auth G] SDF format, chain XA [auth C] SDF format, chain XB [auth E] SDF format, chain XC [auth G] SDF format, chain YA [auth C] SDF format, chain YB [auth E] SDF format, chain YC [auth G] SDF format, chain Z [auth B] SDF format, chain ZB [auth E] SDF format, chain ZC [auth G] MOL2 format, chain AA [auth B] MOL2 format, chain AC [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain BC [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain ED [auth H] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain FD [auth H] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain GD [auth H] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain HD [auth H] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth D] MOL2 format, chain IC [auth F] MOL2 format, chain ID [auth H] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain JC [auth F] MOL2 format, chain JD [auth H] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth D] MOL2 format, chain KC [auth F] MOL2 format, chain KD [auth H] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain LC [auth F] MOL2 format, chain LD [auth H] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain MC [auth F] MOL2 format, chain MD [auth H] MOL2 format, chain N [auth A] MOL2 format, chain NC [auth F] MOL2 format, chain O [auth A] MOL2 format, chain OC [auth F] MOL2 format, chain P [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain TB [auth E] MOL2 format, chain UA [auth C] MOL2 format, chain UB [auth E] MOL2 format, chain VA [auth C] MOL2 format, chain VB [auth E] MOL2 format, chain VC [auth G] MOL2 format, chain WA [auth C] MOL2 format, chain WB [auth E] MOL2 format, chain WC [auth G] MOL2 format, chain XA [auth C] MOL2 format, chain XB [auth E] MOL2 format, chain XC [auth G] MOL2 format, chain YA [auth C] MOL2 format, chain YB [auth E] MOL2 format, chain YC [auth G] MOL2 format, chain Z [auth B] MOL2 format, chain ZB [auth E] MOL2 format, chain ZC [auth G]	AA [auth B] AC [auth E] BA [auth B] BC [auth E] CA [auth B] AA [auth B], AC [auth E], BA [auth B], BC [auth E], CA [auth B], DA [auth B], EA [auth B], ED [auth H], FA [auth B], FB [auth D], FD [auth H], GA [auth B], GB [auth D], GD [auth H], HA [auth B], HB [auth D], HD [auth H], I [auth A], IA [auth B], IB [auth D], IC [auth F], ID [auth H], J [auth A], JA [auth B], JB [auth D], JC [auth F], JD [auth H], K [auth A], KA [auth B], KB [auth D], KC [auth F], KD [auth H], L [auth A], LB [auth D], LC [auth F], LD [auth H], M [auth A], MB [auth D], MC [auth F], MD [auth H], N [auth A], NC [auth F], O [auth A], OC [auth F], P [auth A], SA [auth C], TA [auth C], TB [auth E], UA [auth C], UB [auth E], VA [auth C], VB [auth E], VC [auth G], WA [auth C], WB [auth E], WC [auth G], XA [auth C], XB [auth E], XC [auth G], YA [auth C], YB [auth E], YC [auth G], Z [auth B], ZB [auth E], ZC [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain AC [auth E] Focus chain BA [auth B] Focus chain BC [auth E] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain ED [auth H] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain FD [auth H] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain GD [auth H] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain HD [auth H] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain IC [auth F] Focus chain ID [auth H] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain JC [auth F] Focus chain JD [auth H] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain KC [auth F] Focus chain KD [auth H] Focus chain L [auth A] Focus chain LB [auth D] Focus chain LC [auth F] Focus chain LD [auth H] Focus chain M [auth A] Focus chain MB [auth D] Focus chain MC [auth F] Focus chain MD [auth H] Focus chain N [auth A] Focus chain NC [auth F] Focus chain O [auth A] Focus chain OC [auth F] Focus chain P [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain TB [auth E] Focus chain UA [auth C] Focus chain UB [auth E] Focus chain VA [auth C] Focus chain VB [auth E] Focus chain VC [auth G] Focus chain WA [auth C] Focus chain WB [auth E] Focus chain WC [auth G] Focus chain XA [auth C] Focus chain XB [auth E] Focus chain XC [auth G] Focus chain YA [auth C] Focus chain YB [auth E] Focus chain YC [auth G] Focus chain Z [auth B] Focus chain ZB [auth E] Focus chain ZC [auth G] Interactions & Density Focus chain AA [auth B] Focus chain AC [auth E] Focus chain BA [auth B] Focus chain BC [auth E] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain ED [auth H] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain FD [auth H] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain GD [auth H] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain HD [auth H] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain IC [auth F] Focus chain ID [auth H] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain JC [auth F] Focus chain JD [auth H] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain KC [auth F] Focus chain KD [auth H] Focus chain L [auth A] Focus chain LB [auth D] Focus chain LC [auth F] Focus chain LD [auth H] Focus chain M [auth A] Focus chain MB [auth D] Focus chain MC [auth F] Focus chain MD [auth H] Focus chain N [auth A] Focus chain NC [auth F] Focus chain O [auth A] Focus chain OC [auth F] Focus chain P [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain TB [auth E] Focus chain UA [auth C] Focus chain UB [auth E] Focus chain VA [auth C] Focus chain VB [auth E] Focus chain VC [auth G] Focus chain WA [auth C] Focus chain WB [auth E] Focus chain WC [auth G] Focus chain XA [auth C] Focus chain XB [auth E] Focus chain XC [auth G] Focus chain YA [auth C] Focus chain YB [auth E] Focus chain YC [auth G] Focus chain Z [auth B] Focus chain ZB [auth E] Focus chain ZC [auth G]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain BD [auth G] SDF format, chain CB [auth C] SDF format, chain CD [auth G] SDF format, chain DB [auth C] SDF format, chain EC [auth E] SDF format, chain FC [auth E] SDF format, chain GC [auth E] SDF format, chain OB [auth D] SDF format, chain OD [auth H] SDF format, chain PA [auth B] SDF format, chain PB [auth D] SDF format, chain PC [auth F] SDF format, chain QA [auth B] SDF format, chain QB [auth D] SDF format, chain QC [auth F] SDF format, chain RB [auth D] SDF format, chain RC [auth F] SDF format, chain SC [auth F] SDF format, chain TC [auth F] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain BD [auth G] MOL2 format, chain CB [auth C] MOL2 format, chain CD [auth G] MOL2 format, chain DB [auth C] MOL2 format, chain EC [auth E] MOL2 format, chain FC [auth E] MOL2 format, chain GC [auth E] MOL2 format, chain OB [auth D] MOL2 format, chain OD [auth H] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth D] MOL2 format, chain PC [auth F] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth D] MOL2 format, chain QC [auth F] MOL2 format, chain RB [auth D] MOL2 format, chain RC [auth F] MOL2 format, chain SC [auth F] MOL2 format, chain TC [auth F] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A]	AB [auth C] BB [auth C] BD [auth G] CB [auth C] CD [auth G] AB [auth C], BB [auth C], BD [auth G], CB [auth C], CD [auth G], DB [auth C], EC [auth E], FC [auth E], GC [auth E], OB [auth D], OD [auth H], PA [auth B], PB [auth D], PC [auth F], QA [auth B], QB [auth D], QC [auth F], RB [auth D], RC [auth F], SC [auth F], TC [auth F], U [auth A], V [auth A], W [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain BD [auth G] Focus chain CB [auth C] Focus chain CD [auth G] Focus chain DB [auth C] Focus chain EC [auth E] Focus chain FC [auth E] Focus chain GC [auth E] Focus chain OB [auth D] Focus chain OD [auth H] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain PC [auth F] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain QC [auth F] Focus chain RB [auth D] Focus chain RC [auth F] Focus chain SC [auth F] Focus chain TC [auth F] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain BD [auth G] Focus chain CB [auth C] Focus chain CD [auth G] Focus chain DB [auth C] Focus chain EC [auth E] Focus chain FC [auth E] Focus chain GC [auth E] Focus chain OB [auth D] Focus chain OD [auth H] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain PC [auth F] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain QC [auth F] Focus chain RB [auth D] Focus chain RC [auth F] Focus chain SC [auth F] Focus chain TC [auth F] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]
ALA Query on ALA Download Ideal Coordinates CCD File SDF format, chain DD [auth G] SDF format, chain EB [auth C] SDF format, chain HC [auth E] SDF format, chain PD [auth H] SDF format, chain RA [auth B] SDF format, chain SB [auth D] SDF format, chain UC [auth F] SDF format, chain X [auth A] MOL2 format, chain DD [auth G] MOL2 format, chain EB [auth C] MOL2 format, chain HC [auth E] MOL2 format, chain PD [auth H] MOL2 format, chain RA [auth B] MOL2 format, chain SB [auth D] MOL2 format, chain UC [auth F] MOL2 format, chain X [auth A]	DD [auth G] EB [auth C] HC [auth E] PD [auth H] RA [auth B] DD [auth G], EB [auth C], HC [auth E], PD [auth H], RA [auth B], SB [auth D], UC [auth F], X [auth A]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain DD [auth G] Focus chain EB [auth C] Focus chain HC [auth E] Focus chain PD [auth H] Focus chain RA [auth B] Focus chain SB [auth D] Focus chain UC [auth F] Focus chain X [auth A] Interactions & Density Focus chain DD [auth G] Focus chain EB [auth C] Focus chain HC [auth E] Focus chain PD [auth H] Focus chain RA [auth B] Focus chain SB [auth D] Focus chain UC [auth F] Focus chain X [auth A]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain AD [auth G] SDF format, chain CC [auth E] SDF format, chain DC [auth E] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain NB [auth D] SDF format, chain ND [auth H] SDF format, chain OA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain ZA [auth C] MOL2 format, chain AD [auth G] MOL2 format, chain CC [auth E] MOL2 format, chain DC [auth E] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain ND [auth H] MOL2 format, chain OA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain ZA [auth C]	AD [auth G] CC [auth E] DC [auth E] LA [auth B] MA [auth B] AD [auth G], CC [auth E], DC [auth E], LA [auth B], MA [auth B], NA [auth B], NB [auth D], ND [auth H], OA [auth B], Q [auth A], R [auth A], S [auth A], T [auth A], ZA [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AD [auth G] Focus chain CC [auth E] Focus chain DC [auth E] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain ND [auth H] Focus chain OA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain AD [auth G] Focus chain CC [auth E] Focus chain DC [auth E] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain ND [auth H] Focus chain OA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain ZA [auth C]