1IOO - JenaLib

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Title :   CRYSTAL STRUCTURE OF NICOTIANA ALATA GEMETOPHYTIC SELF-INCOMPATIBILITY ASSOCIATED SF11-RNASE

Authors :   K. Ida, M. Sato, F. Sakiyama, S. Norioka, M. Yamamoto, T. Kumasaka, E. Ya

Date :   26 Mar 01 (Deposition) - 08 May 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Self-Incompatibility Ribonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Ida, S. Norioka, M. Yamamoto, T. Kumasaka, E. Yamashita, E. Newbigin, A. E. Clarke, F. Sakiyama, M. Sato
The 1. 55 A Resolution Structure Of Nicotiana Alata S(F11)-Rnase Associated With Gametophytic Self-Incompatibility.
J. Mol. Biol. V. 314 103 2001
PubMed-ID: 11724536 | Reference-DOI: 10.1006/JMBI.2001.5127

Molecule 1 - SF11-RNASE
	Chains	:	A, B
	Organism Common	:	PERSIAN TOBACCO
	Organism Scientific	:	NICOTIANA ALATA
	Organism Taxid	:	4087

		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 (4, 12)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE

Biological Unit 1 (4, 5)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	XYP	1	Ligand/Ion	BETA-D-XYLOPYRANOSE

Biological Unit 2 (4, 7)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	XYP	1	Ligand/Ion	BETA-D-XYLOPYRANOSE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:28 , LYS A:112 , PHE A:115 , ASP A:116 , NAG A:198 , HOH A:244 , HOH A:247 , HOH A:264 , HOH A:289 , HOH A:440 , HOH A:448 , HOH A:570	BINDING SITE FOR RESIDUE NAG A 197
02	AC2	SOFTWARE	ASP A:113 , LYS A:114 , PHE A:115 , NAG A:197 , BMA A:199 , XYP A:200 , MAN A:201 , HOH A:288 , HOH A:382 , HOH A:555 , HOH B:527	BINDING SITE FOR RESIDUE NAG A 198
03	AC3	SOFTWARE	NAG A:198 , XYP A:200 , MAN A:201 , HOH A:241 , HOH A:263 , HOH A:445 , HOH A:473 , ASP B:175	BINDING SITE FOR RESIDUE BMA A 199
04	AC4	SOFTWARE	NAG A:198 , BMA A:199 , HOH A:241 , HOH A:364 , HOH A:432 , HOH A:532	BINDING SITE FOR RESIDUE XYP A 200
05	AC5	SOFTWARE	ASP A:113 , LYS A:114 , NAG A:198 , BMA A:199 , HOH A:325 , HOH A:328 , HOH A:460 , ASP B:175 , HOH B:499	BINDING SITE FOR RESIDUE MAN A 201
06	AC6	SOFTWARE	ASN B:28 , LYS B:112 , PHE B:115 , ASP B:116 , NAG B:198 , HOH B:261 , HOH B:279 , HOH B:303 , HOH B:514	BINDING SITE FOR RESIDUE NAG B 197
07	AC7	SOFTWARE	GLN A:146 , HOH A:425 , ASP B:113 , PHE B:115 , NAG B:197 , BMA B:199 , XYP B:200 , HOH B:248 , HOH B:302 , HOH B:435 , HOH B:519	BINDING SITE FOR RESIDUE NAG B 198
08	AC8	SOFTWARE	ASP A:175 , SER A:176 , NAG B:198 , XYP B:200 , MAN B:201 , MAN B:203 , HOH B:259 , HOH B:426 , HOH B:556	BINDING SITE FOR RESIDUE BMA B 199
09	AC9	SOFTWARE	LYS B:65 , HIS B:66 , NAG B:198 , BMA B:199 , MAN B:201 , HOH B:259 , HOH B:269 , HOH B:298 , HOH B:314 , HOH B:377 , HOH B:473	BINDING SITE FOR RESIDUE XYP B 200
10	BC1	SOFTWARE	BMA B:199 , XYP B:200 , NAG B:202 , HOH B:246 , HOH B:310 , HOH B:408 , HOH B:419	BINDING SITE FOR RESIDUE MAN B 201
11	BC2	SOFTWARE	ASN A:173 , ASP A:175 , MAN B:201 , HOH B:484 , HOH B:528	BINDING SITE FOR RESIDUE NAG B 202
12	BC3	SOFTWARE	GLN A:146 , ASP A:175 , ASP B:113 , BMA B:199 , HOH B:230 , HOH B:319 , HOH B:457	BINDING SITE FOR RESIDUE MAN B 203

Asymmetric Unit

No.	Residues
1	A:16	-	A:21
2	A:46	-	A:94
3	A:153	-	A:186
4	A:169	-	A:180
5	B:16	-	B:21
6	B:46	-	B:94
7	B:153	-	B:186
8	B:169	-	B:180

Asymmetric Unit

No.	Residues
1	Lys A:47	-	Pro A:48
2	Lys B:47	-	Pro B:48

(no "SAP(SNP)/Variant" information available for 1IOO)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_T2_1	PS00530	Ribonuclease T2 family histidine active site 1.	RNS11_NICAL	29-36	2	A:29-36 B:29-36

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_T2_1	PS00530	Ribonuclease T2 family histidine active site 1.	RNS11_NICAL	29-36	1	A:29-36 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_T2_1	PS00530	Ribonuclease T2 family histidine active site 1.	RNS11_NICAL	29-36	1	- B:29-36

(no "Exon" information available for 1IOO)

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:196
 aligned with RNS11_NICAL | Q7SID5 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      
          RNS11_NICAL     1 DFEYLQLVLTWPASFCYANHCERIAPNNFTIHGLWPDNVKTRLHNCKPKPTYSYFTGKMLNDLDKHWMQLKFEQDYGRTEQPSWKYQYIKHGSCCQKRYNQNTYFGLALRLKDKFDLLRTLQTHRIIPGSSYTFQDIFDAIKTVSQENPDIKCAEVTKGTPELYEIGICFTPNADSMFRCPQSDTCDKTAKVLFRR 196
               SCOP domains d1iooa_ A: Gemetophytic self-incompatibility associated SF11-RNase                                                                                                                                   SCOP domains
               CATH domains 1iooA00 A:1-196 Ribonuclease Rh; Chain A                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhhhh..........eeeeeeee..................hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhh.....eeehhhhhhhhhhhhhh...eeeee.......eeeeeeeee......ee.............eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------RNASE_T2---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ioo A   1 DFEYLQLVLTWPASFCYANHCERIAPNNFTIHGLWPDNVKTRLHNCKPKPTYSYFTGKMLNDLDKHWMQLKFEQDYGRTEQPSWKYQYIKHGSCCQKRYNQNTYFGLALRLKDKFDLLRTLQTHRIIPGSSYTFQDIFDAIKTVSQENPDIKCAEVTKGTPELYEIGICFTPNADSMFRCPQSDTCDKTAKVLFRR 196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:196
 aligned with RNS11_NICAL | Q7SID5 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      
          RNS11_NICAL     1 DFEYLQLVLTWPASFCYANHCERIAPNNFTIHGLWPDNVKTRLHNCKPKPTYSYFTGKMLNDLDKHWMQLKFEQDYGRTEQPSWKYQYIKHGSCCQKRYNQNTYFGLALRLKDKFDLLRTLQTHRIIPGSSYTFQDIFDAIKTVSQENPDIKCAEVTKGTPELYEIGICFTPNADSMFRCPQSDTCDKTAKVLFRR 196
               SCOP domains d1ioob_ B: Gemetophytic self-incompatibility associated SF11-RNase                                                                                                                                   SCOP domains
               CATH domains 1iooB00 B:1-196 Ribonuclease Rh; Chain A                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhhhh..........eeeeeeee..................hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhh.....eeehhhhhhhhhhhhhh...eeeee.......eeeeeeeee......ee.............eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------RNASE_T2---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ioo B   1 DFEYLQLVLTWPASFCYANHCERIAPNNFTIHGLWPDNVKTRLHNCKPKPTYSYFTGKMLNDLDKHWMQLKFEQDYGRTEQPSWKYQYIKHGSCCQKRYNQNTYFGLALRLKDKFDLLRTLQTHRIIPGSSYTFQDIFDAIKTVSQENPDIKCAEVTKGTPELYEIGICFTPNADSMFRCPQSDTCDKTAKVLFRR 196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Ribonuclease Rh-like (20)

Superfamily: Ribonuclease Rh-like (20)

Family: Ribonuclease Rh-like (18)

Protein domain: Gemetophytic self-incompatibility associated SF11-RNase (1)

Winged tobacco (Nicotiana alata) [TaxId: 4087] (1)

1a	d1iooa_	A:
1b	d1ioob_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Ribonuclease Rh; Chain A (18)

Homologous Superfamily: Ribonuclease Rh; Chain A (18)

Persian tobacco (Nicotiana alata) (1)

1a	1iooA00	A:1-196
1b	1iooB00	B:1-196

(no "Pfam Domain" information available for 1IOO)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RNS11_NICAL | Q7SID5)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0033897	ribonuclease T2 activity	Catalysis of the two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides with 2',3'-cyclic phosphate intermediates.
biological process
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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	Cis Peptide Bonds
		Lys A:47 - Pro A:48	[ RasMol ]
		Lys B:47 - Pro B:48	[ RasMol ]

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	1ioo
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1bk7	1BK7 CONTAINS RIBONUCLEASE MC1 FROM THE SEEDS OF BITTER GOURD
1bol	1BOL CONTAINS RIBONUCLEASE RH FROM RHIZOPUS NIVEUS
1dix	1DIX CONTAINS RNASE FROM LYCOPERSICON ESCULENTUM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (12, 12)

SS Bonds (8, 8)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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