2RNF - JenaLib

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Title :   X-RAY CRYSTAL STRUCTURE OF HUMAN RIBONUCLEASE 4 IN COMPLEX WITH D(UP)

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

Date :   03 Nov 98 (Deposition) - 10 Nov 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Ribonuclease, Hydrolase, 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)

Molecule 1 - RIBONUCLEASE 4
	Chains	:	A, B
	EC Number	:	3.1.27.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RNASE 4

		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	UM3	2	Ligand/Ion	2'-DEOXYURIDINE 3'-MONOPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	UM3	1	Ligand/Ion	2'-DEOXYURIDINE 3'-MONOPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	UM3	1	Ligand/Ion	2'-DEOXYURIDINE 3'-MONOPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:7 , GLN A:11 , HIS A:12 , LYS A:40 , PHE A:42 , ASN A:43 , THR A:44 , ARG A:101 , PHE A:117 , GLY A:119 , HOH A:333	BINDING SITE FOR RESIDUE UM3 A 301
2	AC2	SOFTWARE	HIS B:12 , PHE B:42 , ASN B:43 , THR B:44 , ARG B:101 , PHE B:117 , GLY B:119	BINDING SITE FOR RESIDUE UM3 B 302

Asymmetric Unit

No.	Residues
1	A:25	-	A:81
2	A:39	-	A:92
3	A:57	-	A:107
4	A:64	-	A:71
5	B:25	-	B:81
6	B:39	-	B:92
7	B:57	-	B:107
8	B:64	-	B:71

Asymmetric Unit

No.	Residues
1	Ala A:89	-	Pro A:90
2	Asn A:110	-	Pro A:111
3	Ala B:89	-	Pro B:90
4	Asn B:110	-	Pro B:111

(no "SAP(SNP)/Variant" information available for 2RNF)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS4_HUMAN	67-73	2	A:39-45 B:39-45

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS4_HUMAN	67-73	1	A:39-45 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS4_HUMAN	67-73	1	- B:39-45

(no "Exon" information available for 2RNF)

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: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 d2rnfa_ A: Ribonuclease 4                                                                                                SCOP domains
               CATH domains 2rnfA00 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
                 2rnf 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 d2rnfb_ B: Ribonuclease 4                                                                                                SCOP domains
               CATH domains 2rnfB00 B:0-119 P-30 Protein                                                                                             CATH domains
           Pfam domains (1) -RnaseA-2rnfB01 B:1-118                                                                                                - Pfam domains (1)
           Pfam domains (2) -RnaseA-2rnfB02 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
                 2rnf B   0 MQDGMYQRFLRQHVHPEETGGSDRYCNLMMQRRKMTLYHCKRFNTFIHEDIWNIRSICSTTNIQCKNGKMNCHEGVVKVTDCRDTGSSRAPNCRYRAIASTRRVVIACEGNPQVPVHFDG 119
                                     9        19        29        39        49        59        69        79        89        99       109       119

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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: RNase A-like (356)

Superfamily: RNase A-like (356)

Family: Ribonuclease A-like (347)

Protein domain: Ribonuclease 4 (2)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d2rnfa_	A:
1b	d2rnfb_	B:

Asymmetric 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)

Human (Homo sapiens) (46)

1a	2rnfA00	A:0-119
1b	2rnfB00	B:0-119

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: RnaseA] (125)

Family: RnaseA (125)

Homo sapiens (Human) (15)

1a	RnaseA-2rnfB01	B:1-118
1b	RnaseA-2rnfB02	B:1-118

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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	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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(no "Related Entries Specified in the PDB File" available for 2RNF)

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