3D5I - JenaLib

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Title :   CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH EXO-2',3'-CYCLOPHOSPHOROTIOATE

Authors :   V. Bauerova-Hlinkova, J. Sevcik

Date :   16 May 08 (Deposition) - 26 May 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Ribonuclease, Mononucleotide, Protein-Mononucleotide Complex, Exo-2', 3'-Cyclophosphorotioate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Bauerova-Hlinkova, R. Dvorsky, D. Perecko, F. Povazanec, J. Sevci
Structure Of Rnase Sa2 Complexes With Mononucleotides - New Aspects Of Catalytic Reaction And Substrate Recognition
Febs J. V. 276 4156 2009
PubMed-ID: 19558492 | Reference-DOI: 10.1111/J.1742-4658.2009.07125.X

Molecule 1 - RIBONUCLEASE
	Chains	:	A, B, C
	EC Number	:	3.1.4.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEH200
	Expression System Strain	:	NOVABLUE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	STREPTOMYCES AUREOFACIENS
	Organism Taxid	:	1894
	Strain	:	R8/26
	Synonym	:	RIBONUCLEASE SA2

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	SGP	1	Ligand/Ion	GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SGP	-1	Ligand/Ion	GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SGP	1	Ligand/Ion	GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	SGP	-1	Ligand/Ion	GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:34 , GLU A:56 , ARG A:67 , ARG A:71 , HIS A:86 , TYR A:87 , HOH A:121 , ARG C:45	BINDING SITE FOR RESIDUE SO4 A 98
2	AC2	SOFTWARE	SER A:15 , HOH A:150 , GLU B:43 , ARG B:45	BINDING SITE FOR RESIDUE SO4 A 99
3	AC3	SOFTWARE	ARG A:42 , ARG C:67 , ARG C:71 , HIS C:86 , TYR C:87	BINDING SITE FOR RESIDUE SO4 C 98
4	AC4	SOFTWARE	ARG B:34 , VAL B:38 , PHE B:39 , GLU B:40 , ASN B:41 , ARG B:42 , GLU B:43 , GLU B:56 , ARG B:67 , ARG B:71 , HIS B:86 , TYR B:87 , HOH B:129 , HOH B:162	BINDING SITE FOR RESIDUE SGP B 98

Asymmetric Unit

No.	Residues
1	A:9	-	A:97
2	B:9	-	B:97
3	C:9	-	C:97

Asymmetric Unit

No.	Residues
1	Gly A:28	-	Pro A:29
2	Gly B:28	-	Pro B:29
3	Gly C:28	-	Pro C:29

(no "SAP(SNP)/Variant" information available for 3D5I)

(no "PROSITE Motif" information available for 3D5I)

(no "Exon" information available for 3D5I)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:92
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:94
                                    79        89        99       109       119       129       139       149       159    
         Q53752_STRAU    70 ALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d3d5ia_ A: automated matches                                                                   SCOP domains
               CATH domains 3d5iA00 A:4-97  [code=3.10.450.30, no name defined]                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhhhhhhh..........eee..............eeeee.....--.....eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 3d5i A   4 ALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPG--DRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    13        23        33        43        53        63  |     73        83        93    
                                                                                      63 66

Chain B from PDB  Type:PROTEIN  Length:97
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:97
                                    76        86        96       106       116       126       136       146       156       
         Q53752_STRAU    67 ADPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d3d5ib_ B: automated matches                                                                      SCOP domains
               CATH domains 3d5iB00 B:1-97  [code=3.10.450.30, no name defined]                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.hhhhhhhhhhhhhhhh...........ee..............eeeee............eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3d5i B   1 ADPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    10        20        30        40        50        60        70        80        90

Chain C from PDB  Type:PROTEIN  Length:90
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:93
                                    80        90       100       110       120       130       140       150       160   
         Q53752_STRAU    71 LADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d3d5ic_ C: automated matches                                                                  SCOP domains
               CATH domains 3d5iC00 C:5-97  [code=3.10.450.30, no name defined]                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhhh..........eee..............eeeee....---.....eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3d5i C   5 LADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTP---DRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    14        24        34        44        54       | - |      74        84        94   
                                                                                    62  66

Legend:		→ Mismatch	(orange background)
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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 '\|'

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: Bacterial ribonucleases (89)

Protein domain: automated matches (9)

Streptomyces aureofaciens [TaxId: 1894] (8)

1a	d3d5ia_	A:
1b	d3d5ib_	B:
1c	d3d5ic_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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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)

Streptomyces aureofaciens. Organism_taxid: 1894. Strain: r8/26. (4)

1a	3d5iB00	B:1-97
1b	3d5iA00	A:4-97
1c	3d5iC00	C:5-97

(no "Pfam Domain" information available for 3D5I)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q53752_STRAU | Q53752)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:28 - Pro A:29	[ RasMol ]
		Gly B:28 - Pro B:29	[ RasMol ]
		Gly C:28 - Pro C:29	[ RasMol ]

Biological Units
	Complete Structure
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	Q53752_STRAU \| Q53752	:	1py3 1pyl 3d4a 3d5g 3dgy 3dh2

1gmp	STRUCTURE OF RIBONUCLEASE SA WITH 2'-GMP
1py3	STRUCTURE OF RIBONUCLEASE SA2 WITHOUT LIGAND
1pyl	STRUCTURE OF RIBONUCLEASE SA2 WITHOUT LIGAND
1rsn	STRUCTURE OF RIBONUCLEASE SA WITH EXO-2',3'- CYCLOPHOSPHOROTIOATE
2sar	STRUCTURE OF RIBONUCLEASE SA WITH 3'-GMP
3d4a
3d5g

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