1R3M - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE DIMERIC UNSWAPPED FORM OF BOVINE SEMINAL RIBONUCLEASE

Authors :   R. Berisio, F. Sica, C. De Lorenzo, A. Di Fiore, R. Piccoli, A. Zagari, L. Mazzarella

Date :   02 Oct 03 (Deposition) - 18 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Ribonuclease, Swapping, Hinge, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Berisio, F. Sica, C. De Lorenzo, A. Di Fiore, R. Piccoli, A. Zagari, L. Mazzarella
Crystal Structure Of The Dimeric Unswapped Form Of Bovine Seminal Ribonuclease
Febs Lett. V. 554 105 2003
PubMed-ID: 14596923 | Reference-DOI: 10.1016/S0014-5793(03)01114-1
(for further references see the PDB file header)

Molecule 1 - RIBONUCLEASE, SEMINAL
	Chains	:	A, B
	EC Number	:	3.1.27.5
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Secretion	:	SEMINAL FLUID
	Synonym	:	SEMINAL RNASE, S-RNASE, RIBONUCLEASE BS-1

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:11 , HIS A:12 , LYS A:41 , HIS A:119 , PHE A:120 , HOH A:236 , HOH A:356	BINDING SITE FOR RESIDUE PO4 A 125
2	AC2	SOFTWARE	GLN B:11 , HIS B:12 , LYS B:41 , HIS B:119 , PHE B:120 , HOH B:237	BINDING SITE FOR RESIDUE PO4 B 126

Asymmetric Unit

No.	Residues
1	A:26	-	A:84
2	A:31	-	B:32
3	A:32	-	B:31
4	A:40	-	A:95
5	A:58	-	A:110
6	A:65	-	A:72
7	B:26	-	B:84
8	B:40	-	B:95
9	B:58	-	B:110
10	B:65	-	B:72

Asymmetric Unit

No.	Residues
1	Tyr A:92	-	Pro A:93
2	Lys A:113	-	Pro A:114
3	Tyr B:92	-	Pro B:93
4	Lys B:113	-	Pro B:114

(no "SAP(SNP)/Variant" information available for 1R3M)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNS_BOVIN	66-72	2	A:40-46 B:40-46

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNS_BOVIN	66-72	1	A:40-46 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNS_BOVIN	66-72	1	- B:40-46

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	ENSBTAT00000036229	2	ENSBTAE00000284222	chr10:25625986-25626024	39	RNS_BOVIN	-	0	0	-	-
1.3b	ENSBTAT00000036229	3b	ENSBTAE00000284221	chr10:25626721-25627530	810	RNS_BOVIN	1-159	159	2	A:1-124 (gaps) B:1-124 (gaps)	124 124

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:122
 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 d1r3ma_ A: Seminal   ribonucleasease                                                                                         SCOP domains
               CATH domains 1r3mA00 A:1-124 P-3  0 Protein                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh......--..hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3b  PDB: A:1-124 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                   Transcript 1
                 1r3m A   1 KESAAAKFERQHMDSGNSP--SSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10        |- |      30        40        50        60        70        80        90       100       110       120    
                                             19 22

Chain B from PDB  Type:PROTEIN  Length:122
 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 d1r3mb_ B: Seminal   ribonucleasease                                                                                         SCOP domains
               CATH domains 1r3mB00 B:1-124 P-3  0 Protein                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh......--..hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3b  PDB: B:1-124 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                   Transcript 1
                 1r3m B   1 KESAAAKFERQHMDSGNSP--SSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10        |- |      30        40        50        60        70        80        90       100       110       120    
                                             19 22

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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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: RNase A-like (356)

Superfamily: RNase A-like (356)

Family: Ribonuclease A-like (347)

Protein domain: Seminal ribonucleasease (17)

Cow (Bos taurus) [TaxId: 9913] (17)

1a	d1r3ma_	A:
1b	d1r3mb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: P-30 Protein (299)

Homologous Superfamily: P-30 Protein (299)

Cattle (Bos taurus) (152)

1a	1r3mA00	A:1-124
1b	1r3mB00	B:1-124

(no "Pfam Domain" information available for 1R3M)

Asymmetric 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
		Lys A:113 - Pro A:114	[ RasMol ]
		Lys B:113 - Pro B:114	[ RasMol ]
		Tyr A:92 - Pro A:93	[ RasMol ]
		Tyr B:92 - Pro B:93	[ RasMol ]

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1bsr	SWAPPED FORM OF BS-RNASE
1r5c	X-RAY STRUCTURE OF THE COMPLEX OF BOVINE SEMINAL RIBONUCLEASE SWAPPING DIMER WITH D(CPA)
1r5d	X-RAY STRUCTURE OF BOVINE SEMINAL RIBONUCLEASE SWAPPING DIMER FROM A NEW CRYSTAL FORM

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