6KBZ

Crystal structure of yedK with ssDNA containing a tetrahydrofuran abasic site

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0003677	molecular_function	DNA binding
B	0003697	molecular_function	single-stranded DNA binding
B	0005657	cellular_component	replication fork
B	0006508	biological_process	proteolysis
B	0006974	biological_process	DNA damage response
B	0008233	molecular_function	peptidase activity
B	0009432	biological_process	SOS response
B	0016787	molecular_function	hydrolase activity
B	0016829	molecular_function	lyase activity
B	0036297	biological_process	interstrand cross-link repair
B	0097681	biological_process	double-strand break repair via alternative nonhomologous end joining
B	0106300	biological_process	protein-DNA covalent cross-linking repair
B	0140431	molecular_function	DNA-(abasic site) binding
B	0160129	molecular_function	protein-DNA covalent cross-linking activity
D	0003677	molecular_function	DNA binding
D	0003697	molecular_function	single-stranded DNA binding
D	0005657	cellular_component	replication fork
D	0006508	biological_process	proteolysis
D	0006974	biological_process	DNA damage response
D	0008233	molecular_function	peptidase activity
D	0009432	biological_process	SOS response
D	0016787	molecular_function	hydrolase activity
D	0016829	molecular_function	lyase activity
D	0036297	biological_process	interstrand cross-link repair
D	0097681	biological_process	double-strand break repair via alternative nonhomologous end joining
D	0106300	biological_process	protein-DNA covalent cross-linking repair
D	0140431	molecular_function	DNA-(abasic site) binding
D	0160129	molecular_function	protein-DNA covalent cross-linking activity
F	0003677	molecular_function	DNA binding
F	0003697	molecular_function	single-stranded DNA binding
F	0005657	cellular_component	replication fork
F	0006508	biological_process	proteolysis
F	0006974	biological_process	DNA damage response
F	0008233	molecular_function	peptidase activity
F	0009432	biological_process	SOS response
F	0016787	molecular_function	hydrolase activity
F	0016829	molecular_function	lyase activity
F	0036297	biological_process	interstrand cross-link repair
F	0097681	biological_process	double-strand break repair via alternative nonhomologous end joining
F	0106300	biological_process	protein-DNA covalent cross-linking repair
F	0140431	molecular_function	DNA-(abasic site) binding
F	0160129	molecular_function	protein-DNA covalent cross-linking activity
H	0003677	molecular_function	DNA binding
H	0003697	molecular_function	single-stranded DNA binding
H	0005657	cellular_component	replication fork
H	0006508	biological_process	proteolysis
H	0006974	biological_process	DNA damage response
H	0008233	molecular_function	peptidase activity
H	0009432	biological_process	SOS response
H	0016787	molecular_function	hydrolase activity
H	0016829	molecular_function	lyase activity
H	0036297	biological_process	interstrand cross-link repair
H	0097681	biological_process	double-strand break repair via alternative nonhomologous end joining
H	0106300	biological_process	protein-DNA covalent cross-linking repair
H	0140431	molecular_function	DNA-(abasic site) binding
H	0160129	molecular_function	protein-DNA covalent cross-linking activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue MG B 301

Chain	Residue
B	ASP140
B	HOH432
B	HOH436
B	HOH514
B	HOH518
B	HOH581

---

site_id	AC2
Number of Residues	5
Details	binding site for residue MG B 302

Chain	Residue
F	MG301
F	HOH415
B	ASP111
B	HOH462
B	HOH475

---

site_id	AC3
Number of Residues	7
Details	binding site for residue MG F 301

Chain	Residue
B	MG302
B	HOH462
F	ASP140
F	HOH415
F	HOH443
F	HOH496
F	HOH571

---

site_id	AC4
Number of Residues	7
Details	binding site for residue MG H 301

Chain	Residue
D	ASP111
D	HOH303
D	HOH390
H	ASP140
H	HOH491
H	HOH517
H	HOH557

---

site_id	AC5
Number of Residues	16
Details	binding site for Di-nucleotide DT C 1 and 3DR C 2

Chain	Residue
C	DG0
C	DG3
C	HOH104
C	HOH107
C	HOH124
C	HOH128
D	CYS2
D	GLY3
D	ASN75
D	ARG77
D	PHE87
D	THR149
D	ARG162
G	DG0
G	DT1
G	HOH107

---

site_id	AC6
Number of Residues	19
Details	binding site for Di-nucleotide 3DR C 2 and DG C 3

Chain	Residue
C	DT1
C	DA4
C	HOH108
C	HOH110
C	HOH123
C	HOH124
C	HOH128
C	HOH129
D	CYS2
D	GLY3
D	ARG4
D	PRO40
D	ASN75
D	ARG77
D	THR149
D	ARG162
D	VAL211
G	DC7
H	PRO71

---

site_id	AC7
Number of Residues	16
Details	binding site for Di-nucleotide DT E 1 and 3DR E 2

Chain	Residue
A	DG0
A	DT1
E	DG0
E	DG3
E	HOH117
E	HOH123
F	CYS2
F	GLY3
F	ASN75
F	ARG77
F	PHE87
F	THR149
F	HIS160
F	ARG162
F	HOH418
F	HOH436

---

site_id	AC8
Number of Residues	21
Details	binding site for Di-nucleotide 3DR E 2 and DG E 3

Chain	Residue
A	DC7
B	PRO71
E	DT1
E	DA4
E	HOH103
E	HOH104
E	HOH111
E	HOH123
E	HOH124
E	HOH125
E	HOH126
F	CYS2
F	GLY3
F	ARG4
F	PRO40
F	ASN75
F	ARG77
F	THR149
F	HIS160
F	ARG162
F	VAL211

---

site_id	AC9
Number of Residues	18
Details	binding site for Di-nucleotide DT G 1 and 3DR G 2

Chain	Residue
G	DG0
G	DG3
G	HOH103
G	HOH107
G	HOH108
G	HOH113
G	HOH124
G	HOH127
G	HOH135
H	CYS2
H	GLY3
H	ASN75
H	ARG77
H	PHE87
H	THR149
H	ARG162
C	DG0
C	DT1

---

site_id	AD1
Number of Residues	20
Details	binding site for Di-nucleotide 3DR G 2 and DG G 3

Chain	Residue
C	DC7
D	HOH359
G	DT1
G	DA4
G	HOH108
G	HOH111
G	HOH114
G	HOH124
G	HOH127
G	HOH128
G	HOH133
H	CYS2
H	GLY3
H	ARG4
H	PRO40
H	ASN75
H	ARG77
H	THR149
H	ARG162
H	VAL211

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"31235915","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31504793","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"evidences":[{"source":"PubMed","id":"35934051","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"37519246","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	Site: {"description":"Required for sensing abasic sites","evidences":[{"source":"PubMed","id":"31504793","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	Site: {"description":"Required to stabilize abasic sites","evidences":[{"source":"PubMed","id":"31235915","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	4
Details	Modified residue: {"description":"Thiazolidine linkage to a ring-opened DNA abasic site","evidences":[{"source":"PubMed","id":"31235915","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31504793","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---