11BG - JenaLib

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Description

Title :   A POTENTIAL ALLOSTERIC SUBSITE GENERATED BY DOMAIN SWAPPING IN BOVINE SEMINAL RIBONUCLEASE

Authors :   L. Vitagliano, S. Adinolfi, F. Sica, A. Merlino, A. Zagari, L. Mazzarel

Date :   11 Mar 99 (Deposition) - 05 Nov 99 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Hydrolase, Phosphoric Diester, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Vitagliano, S. Adinolfi, F. Sica, A. Merlino, A. Zagari, L. Mazzarella
A Potential Allosteric Subsite Generated By Domain Swapping In Bovine Seminal Ribonuclease.
J. Mol. Biol. V. 293 569 1999
PubMed-ID: 10543951 | Reference-DOI: 10.1006/JMBI.1999.3158
(for further references see the PDB file header)

Compounds

Molecule 1 - PROTEIN (BOVINE SEMINAL RIBONUCLEASE)
	Chains	:	A, B
	EC Number	:	3.1.27.5
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Other Details	:	COMPLEXED WITH 2',5'-UPG
	Other Details - Source	:	BOVINE (BOS TAURUS) SEMINAL FLUID

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 12)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION
2	U2G	4	Ligand/Ion	URIDYLYL-2'-5'-PHOSPHO-GUANOSINE

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION
2	U2G	4	Ligand/Ion	URIDYLYL-2'-5'-PHOSPHO-GUANOSINE

Biological Unit 2 (2, 24)

No.	Name	Count	Type	Full Name
1	SO4	16	Ligand/Ion	SULFATE ION
2	U2G	8	Ligand/Ion	URIDYLYL-2'-5'-PHOSPHO-GUANOSINE

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:11 , HIS A:12 , HOH A:219 , LYS B:41 , HIS B:119 , PHE B:120 , U2G B:133	BINDING SITE FOR RESIDUE SO4 A 125
02	AC2	SOFTWARE	SER A:3 , ALA A:4 , LYS A:39 , LYS A:41 , PRO A:42 , U2G A:132 , HOH A:214	BINDING SITE FOR RESIDUE SO4 A 126
03	AC3	SOFTWARE	LYS A:7 , GLY A:112 , LYS A:113 , HOH A:204 , LYS B:39 , HOH B:244	BINDING SITE FOR RESIDUE SO4 B 127
04	AC4	SOFTWARE	SER A:18 , PRO A:19 , SER A:20 , SER A:21 , SER A:22 , HOH A:316 , GLN B:101	BINDING SITE FOR RESIDUE SO4 A 128
05	AC5	SOFTWARE	SER B:20 , SER B:21 , SER B:22 , SER B:23	BINDING SITE FOR RESIDUE SO4 B 129
06	AC6	SOFTWARE	LYS A:39 , U2G A:132 , HOH A:301 , LYS B:7 , GLY B:112 , LYS B:113 , HOH B:235	BINDING SITE FOR RESIDUE SO4 A 134
07	AC7	SOFTWARE	LYS A:41 , HIS A:119 , PHE A:120 , U2G A:130 , U2G A:132 , HOH A:249 , GLN B:11 , HIS B:12	BINDING SITE FOR RESIDUE SO4 A 135
08	AC8	SOFTWARE	SER B:3 , ALA B:4 , LYS B:39 , PRO B:42 , HOH B:245 , HOH B:263 , HOH B:320	BINDING SITE FOR RESIDUE SO4 B 136
09	AC9	SOFTWARE	VAL A:43 , ASN A:44 , THR A:45 , LYS A:66 , ARG A:85 , LYS A:104 , PHE A:120 , ASP A:121 , ALA A:122 , SER A:123 , U2G A:132 , SO4 A:135 , HOH A:231 , HOH A:295 , HIS B:12	BINDING SITE FOR RESIDUE U2G A 130
10	BC1	SOFTWARE	ASP A:14 , ASN A:24 , ASN A:27 , ASN A:94 , CYS A:95 , HOH A:267 , HOH A:291 , HOH A:318 , CYS B:32 , ARG B:33 , SER B:89 , ASN B:94 , HOH B:302	BINDING SITE FOR RESIDUE U2G A 131
11	BC2	SOFTWARE	LYS A:1 , SER A:3 , LYS A:39 , LYS A:41 , PRO A:42 , SO4 A:126 , U2G A:130 , SO4 A:134 , SO4 A:135 , HOH A:279 , GLN B:11	BINDING SITE FOR RESIDUE U2G A 132
12	BC3	SOFTWARE	HIS A:12 , SO4 A:125 , VAL B:43 , ASN B:44 , THR B:45 , ASN B:67 , ARG B:85 , PHE B:120 , ASP B:121 , ALA B:122 , SER B:123 , HOH B:310 , HOH B:324	BINDING SITE FOR RESIDUE U2G B 133

SS Bonds (10, 10)

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

Cis Peptide Bonds (4, 4)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 11BG)

PROSITE Motifs (1, 2)

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, 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 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNS_BOVIN	66-72	4	A:40-46 B:40-46

Exons (1, 2)

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 B:1-124	124 124

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
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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 d11bga_ A: Seminal ribonucleasease                                                                                           SCOP domains
               CATH domains 11bgA00 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
                 11bg 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 d11bgb_ B: Seminal ribonucleasease                                                                                           SCOP domains
               CATH domains 11bgB00 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
                 11bg B   1 KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10        20        30        40        50        60        70        80        90       100       110       120

Legend:		→ Mismatch	(orange background)
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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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

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: Seminal ribonucleasease (17)

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

1a	d11bga_	A:
1b	d11bgb_	B:

CATH Domains (1, 2)

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)

Cattle (Bos taurus) (152)

1a	11bgA00	A:1-124
1b	11bgB00	B:1-124

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 11BG)

Gene Ontology (11, 11)

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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	11bg
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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 1bsr 1n1x 1n3z 1qwq 1r3m 1r5c 1r5d 1tq9 1y92 1y94 2lfj 3bcm 3bco 3bcp 3djo 3djp 3djq 3djv 3djx 4n4c

Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 11BG)