11BA - JenaLib

Title :   BINDING OF A SUBSTRATE ANALOGUE TO A DOMAIN SWAPPING PROTEIN IN THE COMPLEX OF BOVINE SEMINAL RIBONUCLEASE WITH URIDYLYL-2',5'-ADENOSINE

Authors :   L. Vitagliano, S. Adinolfi, A. Riccio, F. Sica, A. Zagari, L. Mazzarell

Date :   17 Mar 99 (Deposition) - 26 Mar 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.06

Chains :   Asym./Biol. Unit : A,B

Keywords :   Hydrolase, Phosphoric Diester, Rna, 2'-5'-Dinucleotide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Vitagliano, S. Adinolfi, A. Riccio, F. Sica, A. Zagari, L. Mazzarella
Binding Of A Substrate Analog To A Domain Swapping Protein: X-Ray Structure Of The Complex Of Bovine Seminal Ribonuclease With Uridylyl(2', 5')Adenosine.
Protein Sci. V. 7 1691 1998
PubMed-ID: 10082366
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:67 , HIS A:119 , UPA A:125 , HOH A:150 , HOH A:165	BINDING SITE FOR RESIDUE SO4 A 127
2	AC2	SOFTWARE	ASN B:67 , HIS B:119 , UPA B:126 , HOH B:219	BINDING SITE FOR RESIDUE SO4 B 128
3	AC3	SOFTWARE	ASN B:17 , LYS B:113 , PRO B:114 , SER B:115 , HOH B:235 , HOH B:237	BINDING SITE FOR RESIDUE SO4 B 129
4	AC4	SOFTWARE	LYS A:41 , VAL A:43 , ASN A:44 , THR A:45 , ASN A:67 , GLN A:69 , ASN A:71 , ALA A:109 , HIS A:119 , PHE A:120 , SO4 A:127 , HOH A:151 , HOH A:156 , GLN B:11 , HIS B:12	BINDING SITE FOR RESIDUE UPA A 125
5	AC5	SOFTWARE	GLN A:11 , HIS A:12 , HOH A:143 , LYS B:41 , VAL B:43 , ASN B:44 , THR B:45 , CYS B:65 , ASN B:67 , GLN B:69 , ASN B:71 , ALA B:109 , HIS B:119 , PHE B:120 , SO4 B:128 , HOH B:200 , HOH B:212	BINDING SITE FOR RESIDUE UPA B 126
6	AS1	AUTHOR	HIS B:12 , LYS A:41 , THR A:45 , HIS A:119 , PHE A:120 , ASP A:121	COMPOSITE ACTIVE SITE
7	AS2	AUTHOR	HIS B:12 , LYS A:41 , THR A:45 , HIS A:119 , PHE A:120 , ASP A:121	COMPOSITE ACTIVE SITE

SS Bonds (10, 10)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (1, 2)

Sequences/Alignments

Asymmetric/Biological 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:124
 aligned with RNS_BOVIN | P00669 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
            RNS_BOVIN    27 KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 150
               SCOP domains d11baa_ A: Seminal ribonucleasease                                                                                           SCOP domains
               CATH domains 11baA00 A:1-124 P-30 Protein                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh.........hhhhhhhhhhh..........eeeee...hhhhhhhhh.eee........eee....eeeeeeee..........eeeeeeeeeeeee.........eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3b  PDB: A:1-124 UniProt: 1-159 [INCOMPLETE]                                                                          Transcript 1
                 11ba A   1 KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with RNS_BOVIN | P00669 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
            RNS_BOVIN    27 KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 150
               SCOP domains d11bab_ B: Seminal ribonucleasease                                                                                           SCOP domains
               CATH domains 11baB00 B:1-124 P-30 Protein                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh.........hhhhhhhhhhh..........eeeee...hhhhhhhhh.eee........eee....eeeeeeee..........eeeeeeeeeeeee.........eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3b  PDB: B:1-124 UniProt: 1-159 [INCOMPLETE]                                                                          Transcript 1
                 11ba B   1 KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10        20        30        40        50        60        70        80        90       100       110       120

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RNS_BOVIN | P00669)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0004522	ribonuclease A activity	Catalysis of the endonucleolytic cleavage of RNA to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in C-P or U-P 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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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.

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	Cis Peptide Bonds
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