1NBF

Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004843	molecular_function	cysteine-type deubiquitinase activity
A	0016579	biological_process	protein deubiquitination
B	0004843	molecular_function	cysteine-type deubiquitinase activity
B	0016579	biological_process	protein deubiquitination
E	0004843	molecular_function	cysteine-type deubiquitinase activity
E	0016579	biological_process	protein deubiquitination

Functional Information from PROSITE/UniProt

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD

Chain	Residue	Details
C	LYS327-ASP352

---

site_id	PS00972
Number of Residues	16
Details	USP_1 Ubiquitin specific protease (USP) domain signature 1. GLknqGAtCYMNSlLQ

Chain	Residue	Details
A	GLY215-GLN230

---

site_id	PS00973
Number of Residues	18
Details	USP_2 Ubiquitin specific protease (USP) domain signature 2. YiLhAVlvHsGdnhg..GHY

Chain	Residue	Details
A	TYR448-TYR465

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	SITE: Interacts with activating enzyme

Chain	Residue	Details
C	ARG354
C	ARG372
D	ARG354
D	ARG372

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	SITE: Essential for function

Chain	Residue	Details
C	HIS368
D	HIS368
E	HIS464

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291

Chain	Residue	Details
C	SER365
D	SER365

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457

Chain	Residue	Details
C	THR366
D	THR366

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742

Chain	Residue	Details
C	GLZ376
D	GLZ376

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603

Chain	Residue	Details
C	LYS306
D	LYS306

---

site_id	SWS_FT_FI7
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
C	GLZ376
D	GLZ376

---

site_id	SWS_FT_FI8
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144

Chain	Residue	Details
C	LYS311
C	LYS348
D	LYS311
D	LYS348

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860

Chain	Residue	Details
C	LYS327
D	LYS327

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127

Chain	Residue	Details
C	LYS329
D	LYS329

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577

Chain	Residue	Details
C	LYS333
D	LYS333

---

site_id	SWS_FT_FI12
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106

Chain	Residue	Details
C	LYS363
D	LYS363

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	5
Details	a catalytic site defined by CSA, PubMed 12507430

Chain	Residue	Details
A	ASN218
A	CYS223
A	CYS223
A	ASP481
A	HIS464

---

site_id	CSA2
Number of Residues	5
Details	a catalytic site defined by CSA, PubMed 12507430

Chain	Residue	Details
B	ASN218
B	CYS223
B	CYS223
B	ASP481
B	HIS464

---

site_id	CSA3
Number of Residues	5
Details	a catalytic site defined by CSA, PubMed 12507430

Chain	Residue	Details
E	ASN218
E	CYS223
E	CYS223
E	ASP481
E	HIS464

---

site_id	MCSA1
Number of Residues	4
Details	M-CSA 789

Chain	Residue	Details
A	ASN218	electrostatic stabiliser
A	CYS223	nucleofuge, nucleophile, proton acceptor, proton donor
A	HIS464	proton acceptor, proton donor
A	ASP481	electrostatic stabiliser

---

site_id	MCSA2
Number of Residues	4
Details	M-CSA 789

Chain	Residue	Details
B	ASN218	electrostatic stabiliser
B	CYS223	nucleofuge, nucleophile, proton acceptor, proton donor
B	HIS464	proton acceptor, proton donor
B	ASP481	electrostatic stabiliser

---

site_id	MCSA3
Number of Residues	4
Details	M-CSA 789

Chain	Residue	Details
E	ASN218	electrostatic stabiliser
E	CYS223	nucleofuge, nucleophile, proton acceptor, proton donor
E	HIS464	proton acceptor, proton donor
E	ASP481	electrostatic stabiliser

---