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Title :   S1 NUCLEASE FROM ASPERGILLUS ORYZAE, MUTANT D65N, IN COMPLEX WITH PHOSPHATE, 2'-DEOXYCYTIDINE AND 2'-DEOXYGUANOSINE.

Authors :   T. Koval, L. H. Oestergaard, J. Dohnalek

Date :   14 Dec 15 (Deposition) - 28 Dec 16 (Release) - 11 Jan 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.97

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Endonuclease, Zinc Dependent, Complex, Mutant, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Koval, L. H. Stergaard, J. Lehmbeck, A. Nrgaard, P. Lipovova, J. Duskova, T. Skalova, M. Trundova, P. Kolenko, K. Fejfarova, J. Stransky, L. Svecova, J. Hasek, J. Dohnalek
Structural And Catalytic Properties Of S1 Nuclease From Aspergillus Oryzae Responsible For Substrate Recognition, Cleavage, Non-Specificity, And Inhibition.
Plos One V. 11 68832 2016
PubMed-ID: 28036383 | Reference-DOI: 10.1371/JOURNAL.PONE.0168832

Molecule 1 - NUCLEASE S1
	Chains	:	A, B
	EC Number	:	3.1.30.1
	Engineered	:	YES
	Expression System	:	ASPERGILLUS ORYZAE
	Expression System Taxid	:	5062
	Gene	:	NUCS, AO090001000075
	Mutation	:	YES
	Organism Common	:	YELLOW KOJI MOLD
	Organism Scientific	:	ASPERGILLUS ORYZAE RIB40
	Organism Taxid	:	510516
	Other Details	:	MATURE PROTEIN WITHOUT SIGNAL SEQUENCE.
	Synonym	:	DEOXYRIBONUCLEASE S1,ENDONUCLEASE S1,SINGLE-STRANDED- NUCLEATE ENDONUCLEASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 15)

No.	Name	Count	Type	Full Name
1	DCZ	2	Ligand/Ion	2'-DEOXYCYTIDINE
2	GNG	1	Ligand/Ion	2'-DEOXY-GUANOSINE
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	2	Ligand/Ion	PHOSPHATE ION
5	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	DCZ	2	Ligand/Ion	2'-DEOXYCYTIDINE
2	GNG	-1	Ligand/Ion	2'-DEOXY-GUANOSINE
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	1	Ligand/Ion	PHOSPHATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	DCZ	-1	Ligand/Ion	2'-DEOXYCYTIDINE
2	GNG	1	Ligand/Ion	2'-DEOXY-GUANOSINE
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	1	Ligand/Ion	PHOSPHATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:21 , HIS A:26 , ASP A:139 , ZN A:402 , PO4 A:601	binding site for residue ZN A 401
02	AC2	SOFTWARE	ASN A:65 , HIS A:80 , HIS A:135 , ASP A:139 , ZN A:401 , PO4 A:601	binding site for residue ZN A 402
03	AC3	SOFTWARE	HIS A:145 , HIS A:168 , ASP A:172 , PO4 A:601	binding site for residue ZN A 403
04	AC4	SOFTWARE	TRP A:21 , HIS A:26 , ASN A:65 , LYS A:68 , HIS A:80 , HIS A:135 , ASP A:139 , HIS A:145 , ASP A:172 , ZN A:401 , ZN A:402 , ZN A:403 , DCZ A:701 , HOH A:1108 , HOH A:1175	binding site for residue PO4 A 601
05	AC5	SOFTWARE	LYS A:68 , TYR A:69 , PHE A:81 , ASP A:83 , HIS A:145 , ALA A:151 , ASN A:154 , HIS A:168 , PO4 A:601 , HOH A:805 , HOH A:1048 , HOH A:1069 , HOH A:1234	binding site for residue DCZ A 701
06	AC6	SOFTWARE	GLU A:177 , TYR A:183 , HOH A:1032 , LYS B:218 , HOH B:1118	binding site for residue DCZ A 702
07	AC7	SOFTWARE	TRP B:21 , HIS B:26 , ASP B:139 , ZN B:402 , PO4 B:601	binding site for residue ZN B 401
08	AC8	SOFTWARE	ASN B:65 , HIS B:80 , HIS B:135 , ASP B:139 , ZN B:401 , PO4 B:601	binding site for residue ZN B 402
09	AC9	SOFTWARE	HIS B:145 , HIS B:168 , ASP B:172 , PO4 B:601 , HOH B:1034	binding site for residue ZN B 403
10	AD1	SOFTWARE	HOH A:1209 , TRP B:21 , HIS B:26 , ASN B:65 , LYS B:68 , HIS B:80 , HIS B:135 , ASP B:139 , HIS B:145 , ASP B:172 , ZN B:401 , ZN B:402 , ZN B:403 , HOH B:1027 , HOH B:1034 , HOH B:1137	binding site for residue PO4 B 601
11	AD2	SOFTWARE	GLY A:214 , ILE A:226 , PHE B:81 , ASP B:83 , HIS B:145 , ALA B:151 , GLY B:152 , ASN B:154 , HIS B:168 , HOH B:805 , HOH B:1027 , HOH B:1034 , HOH B:1115 , HOH B:1181	binding site for residue GNG B 701
12	AD3	SOFTWARE	PHE A:75 , TYR A:79 , ASN A:112 , TYR A:113 , GLU A:125 , HOH A:1006 , HOH A:1040 , HOH A:1164 , HOH A:1179	binding site for Mono-Saccharide NAG A 501 bound to ASN A 112
13	AD4	SOFTWARE	ASN A:248 , HOH A:1019 , HOH A:1024 , HOH A:1191 , HOH A:1215 , GLU B:255 , ASP B:258 , HOH B:1065	binding site for Mono-Saccharide NAG A 502 bound to ASN A 248
14	AD5	SOFTWARE	PHE B:75 , ASN B:112 , TYR B:113 , HOH B:1032 , HOH B:1070 , HOH B:1071 , HOH B:1217	binding site for Mono-Saccharide NAG B 501 bound to ASN B 112
15	AD6	SOFTWARE	GLU B:197 , LEU B:244 , ALA B:245 , ASN B:248 , HOH B:1012 , HOH B:1093 , HOH B:1122	binding site for Mono-Saccharide NAG B 502 bound to ASN B 248

Asymmetric Unit

No.	Residues
1	A:92	-	A:236
2	A:100	-	A:105
3	B:92	-	B:236
4	B:100	-	B:105

Asymmetric Unit

No.	Residues
1	Pro A:88	-	Pro A:89
2	Pro B:88	-	Pro B:89

(no "SAP(SNP)/Variant" information available for 5FBG)

(no "PROSITE Motif" information available for 5FBG)

(no "Exon" information available for 5FBG)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhh.............hhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fbg A  21 WGNLGHETVAYIAQSFVASSTESFCQNILGDDSTSYLANVATWANTYKYTDAGEFSKPYHFIDAQDNPPQSCGVDYDRDCGSAGCSISAIQNYTNILLESPNGSEALNALKFVVHIIGDIHQPLHDENLEAGGNGIDVTYDGETTNLHHIWDTNMPEEAAGGYSLSVAKTYADLLTERIKTGTYSSKKDSWTDGIDIKDPVSTSMIWAADANTYVCSTVLDDGLAYINSTDLSGEYYDKSQPVFEELIAKAGYRLAAWLDLIASQPS 287
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280

Chain B from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhh.............hhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fbg B  21 WGNLGHETVAYIAQSFVASSTESFCQNILGDDSTSYLANVATWANTYKYTDAGEFSKPYHFIDAQDNPPQSCGVDYDRDCGSAGCSISAIQNYTNILLESPNGSEALNALKFVVHIIGDIHQPLHDENLEAGGNGIDVTYDGETTNLHHIWDTNMPEEAAGGYSLSVAKTYADLLTERIKTGTYSSKKDSWTDGIDIKDPVSTSMIWAADANTYVCSTVLDDGLAYINSTDLSGEYYDKSQPVFEELIAKAGYRLAAWLDLIASQ 285
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5FBG)

(no "CATH Domain" information available for 5FBG)

(no "Pfam Domain" information available for 5FBG)

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	Cis Peptide Bonds
		Pro A:88 - Pro A:89	[ RasMol ]
		Pro B:88 - Pro B:89	[ RasMol ]

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	NUS1_ASPOR \| P24021	:	5fb9 5fba 5fbb 5fbc 5fbd 5fbf

5fb9	5FB9 CONTAINS THE WILD TYPE OF THE SAME PROTEIN WITH UNOCCUPIED ACTIVE SITE
5fba	5FBA CONTAINS THE WILD TYPE OF THE SAME PROTEIN IN COMPLEX WITH PHOSPHATE
5fbb	5FBB CONTAINS THE WILD TYPE OF THE SAME PROTEIN IN COMPLEX WITH PHOSPHATE AND ADENOSINE 5'-MONOPHOSPHATE
5fbc	5FBC CONTAINS THE WILD TYPE OF THE SAME PROTEIN IN COMPLEX WITH 2'- DEOXYADENOSINE-5'-THIO-MONOPHOSPHATE (5'DAMP(S))
5fbd	5FBD CONTAINS THE WILD TYPE OF THE SAME PROTEIN IN COMPLEX WITH PHOSPHATE AND 2'-DEOXYCYTIDINE
5fbf	5FBF CONTAINS THE WILD TYPE OF THE SAME PROTEIN IN COMPLEX WITH TWO MOLECULES OF 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (15, 15)

SS Bonds (4, 4)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (9, 9)

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