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Description

Title :   CRYSTAL STRUCTURE OF THE [S-CARBOXYAMIDOMETHYL-CYS31, S-CARBOXYAMIDOMETHYL-CYS32] MONOMERIC DERIVATIVE OF THE BOVINE SEMINAL RIBONUCLEASE IN THE LIGANDED STATE

Authors :   F. Sica, A. Di Fiore, A. Zagari, L. Mazzarella

Date :   30 Oct 02 (Deposition) - 26 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym./Biol. Unit : A

Keywords :   Protein-Nucleotide Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Sica, A. Di Fiore, A. Zagari, L. Mazzarella
The Unswapped Chain Of Bovine Seminal Ribonuclease: Crystal Structure Of The Free And Liganded Monomeric Derivative
Proteins V. 52 263 2003
PubMed-ID: 12833549 | Reference-DOI: 10.1002/PROT.10407
(for further references see the PDB file header)

Compounds

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

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 4)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	ADN	1	Ligand/Ion	ADENOSINE
2	U3P	1	Ligand/Ion	3'-URIDINEMONOPHOSPHATE
3	YCM	2	Mod. Amino Acid	S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:4 , CYS A:65 , ASN A:71 , ALA A:109 , HIS A:119 , HOH A:219 , HOH A:276 , HOH A:283 , HOH A:295	BINDING SITE FOR RESIDUE ADN A 126
2	AC2	SOFTWARE	GLN A:11 , LYS A:41 , ASN A:44 , THR A:45 , PHE A:120 , HOH A:218 , HOH A:236 , HOH A:271 , HOH A:280 , HOH A:283 , HOH A:305 , HOH A:342 , HOH A:391 , HOH A:434	BINDING SITE FOR RESIDUE U3P A 125

SS Bonds (4, 4)

Asymmetric/Biological Unit

No.	Residues
1	A:26	-	A:84
2	A:40	-	A:95
3	A:58	-	A:110
4	A:65	-	A:72

Cis Peptide Bonds (2, 2)

Asymmetric/Biological Unit

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1N3Z)

PROSITE Motifs (1, 1)

Asymmetric/Biological Unit (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

Exons (1, 1)

Asymmetric/Biological Unit (1, 1)

	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	1	A:1-124 (gaps)	124

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
	(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:119
 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 d1n3za_ A: Semin     al ribonucleasease                                                                                      SCOP domains
               CATH domains 1n3zA00 A:1-124      P-30 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
                 1n3z A   1 KESAAAKFERQHMDSG-----SSNYCNLMMccRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10     |   - |      30||      40        50        60        70        80        90       100       110       120    
                                          16    22       31-YCM                                                                                         
                                                          32-YCM

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, 1)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

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)

d1n3za_

CATH Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

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)

1n3zA00

A:1-124

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 1N3Z)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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 ]
		Tyr A:92 - Pro A:93	[ RasMol ]

Still Images

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	1n3z
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	3.1.27.5
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	RNS_BOVIN \| P00669	:	11ba 11bg 1bsr 1n1x 1qwq 1r3m 1r5c 1r5d 1tq9 1y92 1y94 2lfj 3bcm 3bco 3bcp 3djo 3djp 3djq 3djv 3djx 4n4c

Related Entries Specified in the PDB File

11ba	THE COMPLEX OF BOVINE SEMINAL RIBONUCLEASE WITH URIDYLYL-2' ,5'-ADENOSINE
1bsr	THE SWAPPED ISOMER OF THE BOVINE SEMINAL RIBONUCLEASE
4rsk	STRUCTURE OF THE K7A/R10A/K66A VARIANT OF RIBONUCLEASE A COMPLEXED WITH 3'-UMP