1Q7S - JenaLib

Title :   CRYSTAL STRUCTURE OF BIT1

Authors :   J. M. De Pereda, W. F. Waas, Y. Jan, E. Ruoslahti, P. Schimmel, J. Pascual

Date :   19 Aug 03 (Deposition) - 16 Dec 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. De Pereda, W. F. Waas, Y. Jan, E. Ruoslahti, P. Schimmel, J. Pascual
Crystal Structure Of A Human Peptidyl-Trna Hydrolase Reveals A New Fold And Suggests Basis For A Bifunctional Activity.
J. Biol. Chem. V. 279 8111 2004
PubMed-ID: 14660562 | Reference-DOI: 10.1074/JBC.M311449200
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_073386	Q	85	P	PTH2_HUMAN	Disease (IMNEPD)	730882234	A/B	Q	85	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_073386	Q	85	P	PTH2_HUMAN	Disease (IMNEPD)	730882234	A	Q	85	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_073386	Q	85	P	PTH2_HUMAN	Disease (IMNEPD)	730882234	B	Q	85	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_073386	Q	85	P	PTH2_HUMAN	Disease (IMNEPD)	730882234	A/B	Q	85	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (0, 0)

Exons (1, 2)

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:117
 aligned with PTH2_HUMAN | Q9Y3E5 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:117
                                    72        82        92       102       112       122       132       142       152       162       172       
           PTH2_HUMAN    63 GEYKMILVVRNDLKMGKGKVAAQCSHAAVSAYKQIQRRNPEMLKQWEYCGQPKVVVKAPDEETLIALLAHAKMLGLTVSLIQDAGRTQIAPGSQTVLGIGPGPADLIDKVTGHLKLY 179
               SCOP domains d1q7sa_ A: Bit1 (Cgi-147)                                                                                             SCOP domains
               CATH domains 1q7sA00 A:63-179 Bit1                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh...eeeeee.........eeeeeeeeeeehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------P---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3b  PDB: A:63-179 UniProt: 1-179 [INCOMPLETE]                                                                  Transcript 1
                 1q7s A  63 GEYKMILVVRNDLKMGKGKVAAQCSHAAVSAYKQIQRRNPEMLKQWEYCGQPKVVVKAPDEETLIALLAHAKMLGLTVSLIQDAGRTQIAPGSQTVLGIGPGPADLIDKVTGHLKLY 179
                                    72        82        92       102       112       122       132       142       152       162       172

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with PTH2_HUMAN | Q9Y3E5 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:116
                                    73        83        93       103       113       123       133       143       153       163       173      
           PTH2_HUMAN    64 EYKMILVVRNDLKMGKGKVAAQCSHAAVSAYKQIQRRNPEMLKQWEYCGQPKVVVKAPDEETLIALLAHAKMLGLTVSLIQDAGRTQIAPGSQTVLGIGPGPADLIDKVTGHLKLY 179
               SCOP domains d1q7sb_ B: Bit1 (Cgi-147)                                                                                            SCOP domains
               CATH domains 1q7sB00 B:64-179 Bit1                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh...eeeee..--.......eeeeeeeeeehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------P---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3b  PDB: B:64-179 (gaps) UniProt: 1-179 [INCOMPLETE]                                                          Transcript 1
                 1q7s B  64 EYKMILVVRNDLKMGKGKVAAQCSHAAVSAYKQIQRRNPEMLKQWEYCGQPKVVVKAPDEETLIALLAHAKMLGLTVSLIQDA--TQIAPGSQTVLGIGPGPADLIDKVTGHLKLY 179
                                    73        83        93       103       113       123       133       143  |  | 153       163       173      
                                                                                                            146  |                              
                                                                                                               149

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 (0, 0)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PTH2_HUMAN | Q9Y3E5)

molecular function
	GO:0004045	aminoacyl-tRNA hydrolase activity	Catalysis of the reaction: N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA.
	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: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:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:2000811	negative regulation of anoikis	Any process that stops, prevents or reduces the frequency, rate or extent of anoikis.
	GO:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:2000210	positive regulation of anoikis	Any process that activates or increases the frequency, rate or extent of anoikis.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly A:162 - Pro A:163	[ RasMol ]
		Gly B:162 - Pro B:163	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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