1RNF - JenaLib

Title :   X-RAY CRYSTAL STRUCTURE OF UNLIGANDED HUMAN RIBONUCLEASE 4

Authors :   S. S. Terzyan, R. Peracaula, R. De Llorens, Y. Tsushima, H. Yamada, M. Seno, F. X. Gomis-Rueth, M. Coll

Date :   29 Oct 98 (Deposition) - 29 Oct 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

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

Reference :   S. S. Terzyan, R. Peracaula, R. De Llorens, Y. Tsushima, H. Yamada, M. Seno, F. X. Gomis-Ruth, M. Coll
The Three-Dimensional Structure Of Human Rnase 4, Unliganded And Complexed With D(Up), Reveals The Basis For Its Uridine Selectivity.
J. Mol. Biol. V. 285 205 1999
PubMed-ID: 9878400 | Reference-DOI: 10.1006/JMBI.1998.2288
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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:120
 aligned with RNAS4_HUMAN | P34096 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:120
                                    37        47        57        67        77        87        97       107       117       127       137       147
          RNAS4_HUMAN    28 GQDGMYQRFLRQHVHPEETGGSDRYCNLMMQRRKMTLYHCKRFNTFIHEDIWNIRSICSTTNIQCKNGKMNCHEGVVKVTDCRDTGSSRAPNCRYRAIASTRRVVIACEGNPQVPVHFDG 147
               SCOP domains d1rnfa_ A: Ribonuclease 4                                                                                                SCOP domains
               CATH domains 1rnfA00 A:0-119 P-30 Protein                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.........hhhhhhhhhh..........eeeee...hhhhhhhhh............eeeeeeeeeeeee..........eeeeeeeeeeeee.........eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P-------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rnf A   0 MQDGMYQRFLRQHVHPEETGGSDRYCNLMMQRRKMTLYHCKRFNTFIHEDIWNIRSICSTTNIQCKNGKMNCHEGVVKVTDCRDTGSSRAPNCRYRAIASTRRVVIACEGNPQVPVHFDG 119
                                     9        19        29        39        49        59        69        79        89        99       109       119

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with RNAS4_HUMAN | P34096 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:120
                                    37        47        57        67        77        87        97       107       117       127       137       147
          RNAS4_HUMAN    28 GQDGMYQRFLRQHVHPEETGGSDRYCNLMMQRRKMTLYHCKRFNTFIHEDIWNIRSICSTTNIQCKNGKMNCHEGVVKVTDCRDTGSSRAPNCRYRAIASTRRVVIACEGNPQVPVHFDG 147
               SCOP domains d1rnfb_ B: Ribonuclease 4                                                                                                SCOP domains
               CATH domains 1rnfB00 B:0-119 P-30 Protein                                                                                             CATH domains
           Pfam domains (1) -RnaseA-1rnfB01 B:1-118                                                                                                - Pfam domains (1)
           Pfam domains (2) -RnaseA-1rnfB02 B:1-118                                                                                                - Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhh.........hhhhhhhhhh..........eeeee...hhhhhhhhh............eeeeeeeeeeeee..........eeeeeeeeeeeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P-------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rnf B   0 MQDGMYQRFLRQHVHPEETGGSDRYCNLMMQRRKMTLYHCKRFNTFIHEDIWNIRSICSTTNIQCKNGKMNCHEGVVKVTDCRDTGSSRAPNCRYRAIASTRRVVIACEGNPQVPVHFDG 119
                                     9        19        29        39        49        59        69        79        89        99       109       119

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 (1, 2)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RNAS4_HUMAN | P34096)

molecular function
	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: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.
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
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:0006379	mRNA cleavage	Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:89 - Pro A:90	[ RasMol ]
		Ala B:89 - Pro B:90	[ RasMol ]
		Asn A:110 - Pro A:111	[ RasMol ]
		Asn B:110 - Pro B:111	[ RasMol ]

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