2QB0 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE 2TEL CRYSTALLIZATION MODULE FUSED TO T4 LYSOZYME WITH AN ALA-GLY-PRO LINKER.

Authors :   S. Nauli, J. U. Bowie

Date :   15 Jun 07 (Deposition) - 14 Oct 08 (Release) - 26 Aug 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.56

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

Keywords :   Helical Polymer, Hydrolase Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Nauli, S. Farr, Y. J. Lee, H. Y. Kim, S. Faham, J. U. Bowie
Polymer-Driven Crystallization.
Protein Sci. V. 16 2542 2007
PubMed-ID: 17962407 | Reference-DOI: 10.1110/PS.073074207

Molecule 1 - E80-TELSAM DOMAIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAD-HISA
	Expression System Strain	:	TOP10
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - TELSAM DOMAIN - LYSOZYME CHIMERA
	Chains	:	B, D
	EC Number	:	3.2.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	E
	Organism Scientific	:	ESCHERICHIA COLI, BACTERIOPHAGE T4
	Synonym	:	LYSIS PROTEIN, MURAMIDASE, ENDOLYSIN

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	MN	5	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU D:104	BINDING SITE FOR RESIDUE MN D 256
2	AC2	SOFTWARE	GLU B:104	BINDING SITE FOR RESIDUE MN B 256
3	AC3	SOFTWARE	HIS B:21 , ASP B:33 , ASP B:154 , GLU B:157 , HOH B:277 , HOH B:286	BINDING SITE FOR RESIDUE MN B 257
4	AC4	SOFTWARE	SER C:74 , HIS C:76	BINDING SITE FOR RESIDUE MN C 207
5	AC5	SOFTWARE	ASP D:33 , ASP D:154 , GLU D:157 , HOH D:276	BINDING SITE FOR RESIDUE MN D 257

(no "SS Bond" information available for 2QB0)

Asymmetric Unit

No.	Residues
1	Asn B:95	-	Ile B:96
2	Lys B:153	-	Asp B:154
3	Leu C:64	-	Leu C:65
4	Ala D:92	-	Gly D:93
5	Ala D:134	-	Ala D:135
6	Ala D:135	-	Lys D:136
7	Lys D:136	-	Ser D:137
8	Glu D:138	-	Leu D:139
9	Leu D:139	-	Asp D:140
10	Lys D:141	-	Ala D:142
11	Ile D:143	-	Gly D:144
12	Gly D:144	-	Arg D:145

(no "SAP(SNP)/Variant" information available for 2QB0)

(no "PROSITE Motif" information available for 2QB0)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	ENST00000396373	2	ENSE00001696637	chr12:11903767-11903782	16	ETV6_HUMAN	1-6	6	0	-	-
1.3	ENST00000396373	3	ENSE00001770390	chr12:11904330-11904335	6	ETV6_HUMAN	6-8	3	0	-	-
1.4	ENST00000396373	4	ENSE00001639290	chr12:11904772-11904779	8	ETV6_HUMAN	8-10	3	0	-	-
1.5	ENST00000396373	5	ENSE00002180215	chr12:11905384-11905513	130	ETV6_HUMAN	11-52	42	2	A:15-20 C:15-20	6 6
1.6	ENST00000396373	6	ENSE00001803058	chr12:11992074-11992238	165	ETV6_HUMAN	-	0	0	-	-
1.7	ENST00000396373	7	ENSE00001688954	chr12:12006361-12006495	135	ETV6_HUMAN	-	0	0	-	-
1.8	ENST00000396373	8	ENSE00001700080	chr12:12022358-12022903	546	ETV6_HUMAN	-	0	0	-	-
1.9	ENST00000396373	9	ENSE00001691733	chr12:12037379-12037521	143	ETV6_HUMAN	-	0	0	-	-
1.10	ENST00000396373	10	ENSE00001595848	chr12:12038860-12038960	101	ETV6_HUMAN	-	0	0	-	-
1.11a	ENST00000396373	11a	ENSE00001746849	chr12:12043875-12044063	189	ETV6_HUMAN	-	0	0	-	-

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:77
 aligned with ETV6_HUMAN | P41212 from UniProtKB/Swiss-Prot  Length:452

    Alignment length:77
                                    56        66        76        86        96       106       116       
           ETV6_HUMAN    47 SIRLPAHLRLQPIYWSRDDVAQWLKWAENEFSLRPIDSNTFEMNGKALLLLTKEDFRYRSPHSGDVLYELLQHILKQ 123
               SCOP domains d2qb0a_ A: Etv6 transcription factor pointed domain (Tel SAM)                 SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
               Transcript 1 1.5   ----------------------------------------------------------------------- Transcript 1
                 2qb0 A  15 SIRLPAHLRLQPIYWSRDDVAQWLKWAENEFSLRPIDSNTFEMNGKALLLLTKEDFRYRSPHSGDELYELLQHILKQ  91
                                    24        34        44        54        64        74        84

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:241
                                                                       2                                                                                                                                                                                                     
                                                                      1|                                     3                                                                                                                                                               
                                     -         -         -         -  ||     -         -         -         - |      11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
           ENLYS_BPT4     - ------------------------------------------MN-------------------------------------IFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYK 162
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhh.eeeeee.....eeee..eeee....hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qb0 B  15 SIRLPAHLRLQPIYWSRDDVAQWLKWAENEFSLRPIDSNTFEMNGKALLLLTKEDFRYRSPHSGDVLYELLQHILKQAGPNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFCQDVDAAVRGILRNAKLKPVYDSLDCVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYK 255
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

Chain C from PDB  Type:PROTEIN  Length:77
 aligned with ETV6_HUMAN | P41212 from UniProtKB/Swiss-Prot  Length:452

    Alignment length:77
                                    56        66        76        86        96       106       116       
           ETV6_HUMAN    47 SIRLPAHLRLQPIYWSRDDVAQWLKWAENEFSLRPIDSNTFEMNGKALLLLTKEDFRYRSPHSGDVLYELLQHILKQ 123
               SCOP domains d2qb0c_ C: Etv6 transcription factor pointed domain (Tel SAM)                 SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
               Transcript 1 1.5   ----------------------------------------------------------------------- Transcript 1
                 2qb0 C  15 SIRLPAHLRLQPIYWSRDDVAQWLKWAENEFSLRPIDSNTFEMNGKALLLLTKEDFRYRSPHSGDELYELLQHILKQ  91
                                    24        34        44        54        64        74        84

Chain D from PDB  Type:PROTEIN  Length:241
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:241
                                                                       2                                                                                                                                                                                                     
                                                                      1|                                     3                                                                                                                                                               
                                     -         -         -         -  ||     -         -         -         - |      11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
           ENLYS_BPT4     - ------------------------------------------MN-------------------------------------IFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYK 162
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhh.eeeeee.....eeee..eeee........................hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qb0 D  15 SIRLPAHLRLQPIYWSRDDVAQWLKWAENEFSLRPIDSNTFEMNGKALLLLTKEDFRYRSPHSGDVLYELLQHILKQAGPNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFCQDVDAAVRGILRNAKLKPVYDSLDCVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYK 255
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: SAM domain-like (639)

Superfamily: SAM/Pointed domain (61)

Family: Pointed domain (12)

Protein domain: Etv6 transcription factor pointed domain (Tel SAM) (5)

Escherichia coli [TaxId: 562] (3)

1a	d2qb0a_	A:
1b	d2qb0c_	C:

(no "CATH Domain" information available for 2QB0)

(no "Pfam Domain" information available for 2QB0)

Asymmetric Unit(hide GO term definitions)

Chain A,C (ETV6_HUMAN | P41212)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	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).
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
	GO:0001227	transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in the regulatory region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0071425	hematopoietic stem cell proliferation	The expansion of a hematopoietic stem cell population by cell division. A hematopoietic stem cell is a stem cell from which all cells of the lymphoid and myeloid lineages develop.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain B,D (ENLYS_BPT4 | P00720)

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: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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0003796	lysozyme activity	Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
biological process
	GO:0016998	cell wall macromolecule catabolic process	The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	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:0009253	peptidoglycan catabolic process	The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0019076	viral release from host cell	The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.

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	Cis Peptide Bonds
		Ala D:134 - Ala D:135	[ RasMol ]
		Ala D:135 - Lys D:136	[ RasMol ]
		Ala D:92 - Gly D:93	[ RasMol ]
		Asn B:95 - Ile B:96	[ RasMol ]
		Glu D:138 - Leu D:139	[ RasMol ]
		Gly D:144 - Arg D:145	[ RasMol ]
		Ile D:143 - Gly D:144	[ RasMol ]
		Leu C:64 - Leu C:65	[ RasMol ]
		Leu D:139 - Asp D:140	[ RasMol ]
		Lys B:153 - Asp B:154	[ RasMol ]
		Lys D:136 - Ser D:137	[ RasMol ]
		Lys D:141 - Ala D:142	[ RasMol ]

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	2qb0
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	ETV6_HUMAN \| P41212
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2qar	THE SAME 2TEL MODULE FUSED TO T4 LYSOZYME USING A 3-RESIDUE LINKER.
2qb1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (1, 2)

Sequences/Alignments

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SCOP Domains (1, 2)

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Pfam Domains (0, 0)

Gene Ontology (31, 31)

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Related Entries Specified in the PDB File