1ZX2 - JenaLib

Title :   CRYSTAL STRUCTURE OF YEAST UBP3-ASSOCIATED PROTEIN BRE5

Authors :   K. Li, K. Zhao, B. Ossareh-Nazari, G. Da, C. Dargemont, R. Marmorstein

Date :   06 Jun 05 (Deposition) - 21 Jun 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ubp3, Deubiqutinate, Ntf2, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Li, K. Zhao, B. Ossareh-Nazari, G. Da, C. Dargemont, R. Marmorstein
Structural Basis For Interaction Between The Ubp3 Deubiquitinating Enzyme And Its Bre5 Cofactor
J. Biol. Chem. V. 280 29176 2005
PubMed-ID: 15955808 | Reference-DOI: 10.1074/JBC.M502975200
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (1, 2)

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
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Chain A from PDB  Type:PROTEIN  Length:130
 aligned with BRE5_YEAST | P53741 from UniProtKB/Swiss-Prot  Length:515

    Alignment length:142
                             1                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139  
           BRE5_YEAST     - -MGVTVQDICFAFLQNYYERMRTDPSKLAYFYASTAELTHTNYQSKSTNEKDDVLPTVKVTGRENINKFFSRNDAKVRSLKLKLDTIDFQYTGHLHKSILIMATGEMFWTGTPVYKFCQTFILLPSSNGSTFDITNDIIRFI 141
               SCOP domains -d1zx2a1 A:1-141 UBP3-associated protein BR            E5                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee..------------.eeeeehhhhhhhhhhhhhhhhhheeeeeeeeeeeeehhhhheeeeeeeeeeee.....eeeeeeeeeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------NTF2_DOMAIN  PDB: A:8-140 UniProt: 8-140                                                                                             - PROSITE
               Transcript 1 -Exon 1.1  PDB: A:1-141 (gaps) UniProt: 1-515 [INCOMPLETE]                                                                                     Transcript 1
                 1zx2 A   0 SMGVTVQDICFAFLQNYYERMRTDPSKLAYFYASTAELTHTNY------------PTVKVTGRENINKFFSRNDAKVRSLKLKLDTIDFQYTGHLHKSILIMATGEMFWTGTPVYKFCQTFILLPSSNGSTFDITNDIIRFI 141
                                     9        19        29        39  |      -     |  59        69        79        89        99       109       119       129       139  
                                                                     42           55

Chain B from PDB  Type:PROTEIN  Length:130
 aligned with BRE5_YEAST | P53741 from UniProtKB/Swiss-Prot  Length:515

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
           BRE5_YEAST     2 GVTVQDICFAFLQNYYERMRTDPSKLAYFYASTAELTHTNYQSKSTNEKDDVLPTVKVTGRENINKFFSRNDAKVRSLKLKLDTIDFQYTGHLHKSILIMATGEMFWTGTPVYKFCQTFILLPSSNGSTFDITNDIIRFISN 143
               SCOP domains d1zx2b_ B: UBP3-associated protein BRE5                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------NTF2-1zx2B01 B:8-140                                                                                                                 --- Pfam domains (1)
           Pfam domains (2) ------NTF2-1zx2B02 B:8-140                                                                                                                 --- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee..------------.eeeeehhhhhhhhhhhhhhhhhheeeeeeeeeeeeehhhhheeeeeeeeeeee..eeeeeeeeeeeeee......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------NTF2_DOMAIN  PDB: B:8-140 UniProt: 8-140                                                                                             --- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-143 (gaps) UniProt: 1-515 [INCOMPLETE]                                                                                      Transcript 1
                 1zx2 B   2 GVTVQDICFAFLQNYYERMRTDPSKLAYFYASTAELTHTNY------------PTVKVTGRENINKFFSRNDAKVRSLKLKLDTIDFQYTGHLHKSILIMATGEMFWTGTPVYKFCQTFILLPSSNGSTFDITNDIIRFISN 143
                                    11        21        31        41|        -   |    61        71        81        91       101       111       121       131       141  
                                                                   42           55

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)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BRE5_YEAST | P53741)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0016579	protein deubiquitination	The removal of one or more ubiquitin groups from a protein.
	GO:0060628	regulation of ER to Golgi vesicle-mediated transport	Any process that modulates the rate, frequency, or extent of ER to Golgi vesicle-mediated transport, the directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
	GO:2000156	regulation of retrograde vesicle-mediated transport, Golgi to ER	Any process that modulates the frequency, rate or extent of retrograde vesicle-mediated transport, Golgi to ER.
	GO:0034517	ribophagy	The process in which cells degrade mature ribosomes under conditions of starvation.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:1990861	Ubp3-Bre5 deubiquitination complex	A protein complex that cleaves ubiquitin from specific substrates. In the budding yeast Saccharomyces cerevisiae, this complex consists of Ubp3p and Bre5p.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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