3AHS - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF USTILAGO SPHAEROGENA RIBONUCLEASE U2B

Authors :   S. Noguchi

Date :   29 Apr 10 (Deposition) - 07 Jul 10 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.32

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Purine-Specific Endo-Ribonuclease, Hydrolase, Isoaspartate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Noguchi
Structural Changes Induced By The Deamidation And Isomerization Of Asparagine Revealed By The Crystal Structure Of Ustilago Sphaerogena Ribonuclease U2B
Biopolymers V. 93 1003 2010
PubMed-ID: 20623666 | Reference-DOI: 10.1002/BIP.21514

Molecule 1 - RIBONUCLEASE U2
	Chains	:	A, B, C
	EC Number	:	3.1.27.4
	Organism Common	:	SMUT FUNGUS
	Organism Scientific	:	USTILAGO SPHAEROGENA
	Organism Taxid	:	5271
	Synonym	:	RNASE U2

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	IAS	2	Mod. Amino Acid	BETA-L-ASPARTIC ACID
3	K	2	Ligand/Ion	POTASSIUM ION
4	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	IAS	1	Mod. Amino Acid	BETA-L-ASPARTIC ACID
3	K	-1	Ligand/Ion	POTASSIUM ION
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	IAS	1	Mod. Amino Acid	BETA-L-ASPARTIC ACID
3	K	-1	Ligand/Ion	POTASSIUM ION
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	IAS	-1	Mod. Amino Acid	BETA-L-ASPARTIC ACID
3	K	-1	Ligand/Ion	POTASSIUM ION
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:39 , HIS A:41 , GLU A:62 , ARG A:85 , HIS A:101 , PHE A:110 , HOH A:247 , HOH A:382 , HOH A:488 , TYR C:78	BINDING SITE FOR RESIDUE PO4 A 115
2	AC2	SOFTWARE	ASP A:28 , VAL A:30 , GLY A:33 , HOH A:505	BINDING SITE FOR RESIDUE K A 116
3	AC3	SOFTWARE	TYR B:39 , HIS B:41 , GLU B:62 , TYR B:78 , ARG B:85 , HIS B:101 , PHE B:110 , HOH B:258 , HOH B:282 , HOH B:390	BINDING SITE FOR RESIDUE PO4 B 115
4	AC4	SOFTWARE	ASP B:28 , VAL B:30 , GLY B:33 , HOH B:427	BINDING SITE FOR RESIDUE K B 116
5	AC5	SOFTWARE	TYR A:78 , TYR C:39 , HIS C:41 , GLU C:62 , ARG C:85 , HIS C:101 , PHE C:110 , HOH C:305 , HOH C:320 , HOH C:438	BINDING SITE FOR RESIDUE PO4 C 115
6	AC6	SOFTWARE	GLY B:10 , THR B:102 , GLY B:103 , THR B:111 , GLY C:10 , GLY C:11 , ASN C:12 , THR C:102 , HOH C:294 , HOH C:329 , HOH C:367 , HOH C:481	BINDING SITE FOR RESIDUE GOL C 201
7	AC7	SOFTWARE	TYR A:44 , GLU A:46 , HOH A:437	BINDING SITE FOR RESIDUE GOL A 202

Asymmetric Unit

No.	Residues
1	A:1	-	A:54
2	A:9	-	A:113
3	A:55	-	A:96
4	B:1	-	B:54
5	B:9	-	B:113
6	B:55	-	B:96
7	C:1	-	C:54
8	C:9	-	C:113
9	C:55	-	C:96

Asymmetric Unit

No.	Residues
1	Tyr A:39	-	Pro A:40
2	Gly A:58	-	Pro A:59
3	Gly A:69	-	Pro A:70
4	Tyr B:39	-	Pro B:40
5	Gly B:58	-	Pro B:59
6	Gly B:69	-	Pro B:70
7	Tyr C:39	-	Pro C:40
8	Gly C:58	-	Pro C:59
9	Gly C:69	-	Pro C:70

(no "SAP(SNP)/Variant" information available for 3AHS)

(no "PROSITE Motif" information available for 3AHS)

(no "Exon" information available for 3AHS)

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:114
 aligned with RNU2_USTSP | P00654 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:114
                                    10        20        30        40        50        60        70        80        90       100       110    
           RNU2_USTSP     1 CDIPQSTNCGGNVYSNDDINTAIQGALDDVANGDRPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVSPGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS 114
               SCOP domains d3ahsa_ A: RNase U2                                                                                                SCOP domains
               CATH domains 3ahsA00 A:1-114  [code=3.10.450.30, no name defined]                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee..eeeehhhhhhhhhhhhh............ee.................eeeee...................eeeeee.....eeeeee..........ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3ahs A   1 CDIPQSTNCGGNVYSNDDINTAIQGALDDVAxGDRPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVSPGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS 114
                                    10        20        30 |      40        50        60        70        80        90       100       110    
                                                          32-IAS

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with RNU2_USTSP | P00654 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:114
                                    10        20        30        40        50        60        70        80        90       100       110    
           RNU2_USTSP     1 CDIPQSTNCGGNVYSNDDINTAIQGALDDVANGDRPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVSPGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS 114
               SCOP domains d3ahsb_ B: RNase U2                                                                                                SCOP domains
               CATH domains 3ahsB00 B:1-114  [code=3.10.450.30, no name defined]                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee..eeeehhhhhhhhhhhhh............eee................eeeee...................eeeeee.....eeeeee..........ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3ahs B   1 CDIPQSTNCGGNVYSNDDINTAIQGALDDVAxGDRPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVSPGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS 114
                                    10        20        30 |      40        50        60        70        80        90       100       110    
                                                          32-IAS

Chain C from PDB  Type:PROTEIN  Length:108
 aligned with RNU2_USTSP | P00654 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:114
                                    10        20        30        40        50        60        70        80        90       100       110    
           RNU2_USTSP     1 CDIPQSTNCGGNVYSNDDINTAIQGALDDVANGDRPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVSPGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS 114
               SCOP domains d3ahsc_ C: RNase U2                                                                                                SCOP domains
               CATH domains 3ahsC00 C:1-114  [code=3.10.      450.30, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee..eeeehhhhhhhhhhhhh------......ee.................eeeee...................eeeeee.....eeeeee..........ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3ahs C   1 CDIPQSTNCGGNVYSNDDINTAIQGALD------RPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVSPGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS 114
                                    10        20       | -    |   40        50        60        70        80        90       100       110    
                                                      28     35

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Microbial ribonucleases (174)

Superfamily: Microbial ribonucleases (174)

Family: Fungal ribonucleases (79)

Protein domain: RNase U2 (5)

Ustilago sphaerogena [TaxId: 5271] (5)

1a	d3ahsa_	A:
1b	d3ahsb_	B:
1c	d3ahsc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Nuclear Transport Factor 2; Chain: A, (517)

Homologous Superfamily: [code=3.10.450.30, no name defined] (159)

Smut fungus (Ustilago sphaerogena) (4)

1a	3ahsC00	C:1-114
1b	3ahsA00	A:1-114
1c	3ahsB00	B:1-114

(no "Pfam Domain" information available for 3AHS)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RNU2_USTSP | P00654)

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:0004521	endoribonuclease activity	Catalysis of the hydrolysis of ester linkages within ribonucleic acid 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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0033899	ribonuclease U2 activity	Catalysis of the two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Ap or Gp with 2',3'-cyclic phosphate intermediates.
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:58 - Pro A:59	[ RasMol ]
		Gly A:69 - Pro A:70	[ RasMol ]
		Gly B:58 - Pro B:59	[ RasMol ]
		Gly B:69 - Pro B:70	[ RasMol ]
		Gly C:58 - Pro C:59	[ RasMol ]
		Gly C:69 - Pro C:70	[ RasMol ]
		Tyr A:39 - Pro A:40	[ RasMol ]
		Tyr B:39 - Pro B:40	[ RasMol ]
		Tyr C:39 - Pro C:40	[ RasMol ]

Biological Units
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	3ahs
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	RNU2_USTSP \| P00654
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	3.1.27.4
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UniProtKB/Swiss-Prot
	RNU2_USTSP \| P00654	:	1rtu 3agn 3ago 3ahw

1rtu	SAME PROTEIN WITH ORIGINAL ASN32 AND ISOASPARTATE AT RESIDUE 45 AND
3agn	SAME PROTEIN WITH ORIGINAL ASN32, COMPLEXED WITH ADENOSINE- 3'-MONOPHOSPHATE
3ago	SAME PROTEIN WITH ORIGINAL ASN32, COMPLEXED WITH ADENOSINE- 3'-MONOPHOSPHATE
3ahw	SAME PROTEIN WITH ORIGINAL ASN32, COMPLEXED WITH ADENOSINE 2'-MONOPHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (7, 7)

SS Bonds (9, 9)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 3)

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Pfam Domains (0, 0)

Gene Ontology (11, 11)

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