4E2T - JenaLib

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Title :   CRYSTAL STRUCTURES OF RADA INTEIN FROM PYROCOCCUS HORIKOSHII

Authors :   J. S. Oeemig, D. Zhou, T. Kajander, A. Wlodawer, H. Iwai

Date :   09 Mar 12 (Deposition) - 16 May 12 (Release) - 25 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Intein, Hint-Fold, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. S. Oeemig, D. Zhou, T. Kajander, A. Wlodawer, H. Iwai
Nmr And Crystal Structures Of The Pyrococcus Horikoshii Rad Intein Guide A Strategy For Engineering A Highly Efficient And Promiscuous Intein.
J. Mol. Biol. V. 421 85 2012
PubMed-ID: 22560994 | Reference-DOI: 10.1016/J.JMB.2012.04.029

Molecule 1 - PHO RADA INTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKRRS15
	Expression System Strain	:	ER2566
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RADA, PH0263
	Mutation	:	YES
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
	Synonym	:	DNA REPAIR AND RECOMBINATION PROTEIN RADA

		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 (2, 5)

No.	Name	Count	Type	Full Name
1	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	GOL	4	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	EPE	-1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GOL A:202 , PHE B:37 , TYR B:69 , ASP B:153 , VAL B:155	BINDING SITE FOR RESIDUE EPE A 201
2	AC2	SOFTWARE	EPE A:201 , HOH A:339	BINDING SITE FOR RESIDUE GOL A 202
3	AC3	SOFTWARE	SER A:83 , HOH A:343 , GLU B:74	BINDING SITE FOR RESIDUE GOL A 203
4	AC4	SOFTWARE	SER A:83 , PHE A:136 , HIS A:137 , GLU A:138 , HOH A:321 , HOH A:361 , GLU B:74 , LYS B:75 , HOH B:313	BINDING SITE FOR RESIDUE GOL A 204
5	AC5	SOFTWARE	GLU A:74 , LYS A:75 , ASN A:148 , HOH A:345 , LYS B:72 , SER B:82 , SER B:83 , GLU B:138 , TRP B:150	BINDING SITE FOR RESIDUE GOL B 201

(no "SS Bond" information available for 4E2T)

(no "Cis Peptide Bond" information available for 4E2T)

(no "SAP(SNP)/Variant" information available for 4E2T)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTEIN_N_TER	PS50817	Intein N-terminal splicing motif profile.	RADA_PYRHO	153-249	2	A:2-97 B:2-97
2	INTEIN_C_TER	PS50818	Intein C-terminal splicing motif profile.	RADA_PYRHO	302-325	2	A:150-172 B:150-172

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTEIN_N_TER	PS50817	Intein N-terminal splicing motif profile.	RADA_PYRHO	153-249	1	A:2-97 -
2	INTEIN_C_TER	PS50818	Intein C-terminal splicing motif profile.	RADA_PYRHO	302-325	1	A:150-172 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTEIN_N_TER	PS50817	Intein N-terminal splicing motif profile.	RADA_PYRHO	153-249	1	- B:2-97
2	INTEIN_C_TER	PS50818	Intein C-terminal splicing motif profile.	RADA_PYRHO	302-325	1	- B:150-172

(no "Exon" information available for 4E2T)

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)
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Chain A from PDB  Type:PROTEIN  Length:172
 aligned with RADA_PYRHO | O58001 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:172
                                   162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322  
           RADA_PYRHO   153 CFARDTEVYYENDTVPHMESIEEMYSKYASMNGELPFDNGYAVPLDNVFVYTLDIASGEIKKTRASYIYREKVEKLIEIKLSSGYSLKVTPSHPVLLFRDGLQWVPAAEVKPGDVVVGVREEVLRRRIISKGELEFHEVSSVRIIDYNNWVYDLVIPETHNFIAPNGLVLHN 324
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeeee..eeeeeehhhhhhhhhhhhh.eee..eeeeeeeeeeeeee......eeeeeeeeeeeeeeeeeeeeee....eeee....eeeee...eeeee.hhh....eeeee.hhhhhh.......eeeeeeeeeeeeeeeeeeeeee.....eee.....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE INTEIN_N_TER  PDB: A:2-97 UniProt: 153-249                                                       ----------------------------------------------------INTEIN_C_TER            PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e2t A   1 AFARDTEVYYENDTVPHMESIEEMYSKYASMNGELPFDNGYAVPLDNVFVYTLDIASGEIKKTRASYIYREKVEKLIEIKLSSGYSLKVTPSHPVLLFRDGLQWVPAAEVKPGDVVVGVREEVLRRRIISKGELEFHEVSSVRIIDYNNWVYDLVIPETHNFIAPNGLVLHN 172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with RADA_PYRHO | O58001 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:172
                                   162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322  
           RADA_PYRHO   153 CFARDTEVYYENDTVPHMESIEEMYSKYASMNGELPFDNGYAVPLDNVFVYTLDIASGEIKKTRASYIYREKVEKLIEIKLSSGYSLKVTPSHPVLLFRDGLQWVPAAEVKPGDVVVGVREEVLRRRIISKGELEFHEVSSVRIIDYNNWVYDLVIPETHNFIAPNGLVLHN 324
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeee......eeeehhhhhhhhhhhhh.eee..eeeee....eeeeee....eeeeee..eeeeeeeeeeeeeee....eeee....eeeee...eeeee.hhh....eeeee.hhhh..---....eeeeeeeeeeeeeeeeeeeeee.....eee.....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE INTEIN_N_TER  PDB: B:2-97 UniProt: 153-249                                                       ----------------------------------------------------INTEIN_C_TER            PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e2t B   1 AFARDTEVYYENDTVPHMESIEEMYSKYASMNGELPFDNGYAVPLDNVFVYTLDIASGEIKKTRASYIYREKVEKLIEIKLSSGYSLKVTPSHPVLLFRDGLQWVPAAEVKPGDVVVGVREEVLRR---SKGELEFHEVSSVRIIDYNNWVYDLVIPETHNFIAPNGLVLHN 172
                                    10        20        30        40        50        60        70        80        90       100       110       120     | 130       140       150       160       170  
                                                                                                                                                       126 130

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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 '\|'

(no "SCOP Domain" information available for 4E2T)

(no "CATH Domain" information available for 4E2T)

(no "Pfam Domain" information available for 4E2T)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RADA_PYRHO | O58001)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008094	DNA-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0016539	intein-mediated protein splicing	The removal of an internal amino acid sequence (an intein) from a protein during protein maturation; the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues.

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	4e2t
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	RADA_PYRHO \| O58001	:	2lqm 4e2u

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