1ZY7 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF AN ADENOSINE DEAMINASE THAT ACTS ON RNA (HADAR2) BOUND TO INOSITOL HEXAKISPHOSPHATE (IHP)

Authors :   M. R. Macbeth, H. L. Schubert, A. P. Vandemark, A. T. Lingam, C. P. Hill, B. L. Bass

Date :   09 Jun 05 (Deposition) - 13 Sep 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Alpha/Beta Deaminase Motif, Zinc Coordination, Ionsitol Hexakisphosphate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. R. Macbeth, H. L. Schubert, A. P. Vandemark, A. T. Lingam, C. P. Hill, B. L. Bass
Inositol Hexakisphosphate Is Bound In The Adar2 Core And Required For Rna Editing.
Science V. 309 1534 2005
PubMed-ID: 16141067 | Reference-DOI: 10.1126/SCIENCE.1113150
(for further references see the PDB file header)

Molecule 1 - RNA-SPECIFIC ADENOSINE DEAMINASE B1, ISOFORM DRADA2A
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Strain	:	BCY123
	Expression System Taxid	:	4932
	Expression System Vector	:	PJELTRC6
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		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 (3, 5)

No.	Name	Count	Type	Full Name
1	IHP	2	Ligand/Ion	INOSITOL HEXAKISPHOSPHATE
2	SO4	1	Ligand/Ion	SULFATE ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	IHP	1	Ligand/Ion	INOSITOL HEXAKISPHOSPHATE
2	SO4	-1	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	IHP	1	Ligand/Ion	INOSITOL HEXAKISPHOSPHATE
2	SO4	1	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:394 , CYS A:451 , LYS A:483 , CYS A:516 , HOH A:1274	BINDING SITE FOR RESIDUE ZN A 801
2	AC2	SOFTWARE	HIS B:394 , CYS B:451 , LYS B:483 , CYS B:516 , HOH B:1166	BINDING SITE FOR RESIDUE ZN B 802
3	AC3	SOFTWARE	SER B:384 , ARG B:386 , LYS B:618 , HOH B:1089	BINDING SITE FOR RESIDUE SO4 B 903
4	AC4	SOFTWARE	ASN A:391 , ILE A:397 , ARG A:400 , ARG A:401 , THR A:513 , LYS A:519 , ARG A:522 , GLY A:530 , SER A:531 , LYS A:629 , TYR A:658 , LYS A:662 , TYR A:668 , LYS A:672 , TRP A:687 , GLU A:689 , LYS A:690 , ASP A:695 , HOH A:903 , HOH A:904 , HOH A:908 , HOH A:909 , HOH A:913 , HOH A:914 , HOH A:915 , HOH A:917 , HOH A:925 , HOH A:932 , HOH A:939 , HOH A:993 , HOH A:1004 , HOH A:1017 , HOH A:1055 , HOH A:1066 , HOH A:1276	BINDING SITE FOR RESIDUE IHP A 901
5	AC5	SOFTWARE	ASN B:391 , ILE B:397 , ARG B:400 , ARG B:401 , THR B:513 , LYS B:519 , ARG B:522 , GLY B:530 , SER B:531 , LYS B:629 , TYR B:658 , LYS B:662 , TYR B:668 , LYS B:672 , TRP B:687 , GLU B:689 , LYS B:690 , ASP B:695 , HOH B:905 , HOH B:906 , HOH B:910 , HOH B:911 , HOH B:915 , HOH B:918 , HOH B:921 , HOH B:922 , HOH B:926 , HOH B:932 , HOH B:949 , HOH B:957 , HOH B:961 , HOH B:969 , HOH B:975 , HOH B:990 , HOH B:1036 , HOH B:1050	BINDING SITE FOR RESIDUE IHP B 902

(no "SS Bond" information available for 1ZY7)

Asymmetric Unit

No.	Residues
1	Pro B:592	-	Gly B:593

(no "SAP(SNP)/Variant" information available for 1ZY7)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	A_DEAMIN_EDITASE	PS50141	Adenosine to inosine editase domain profile.	RED1_HUMAN	370-737	2	A:370-697 B:370-697

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	A_DEAMIN_EDITASE	PS50141	Adenosine to inosine editase domain profile.	RED1_HUMAN	370-737	1	A:370-697 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	A_DEAMIN_EDITASE	PS50141	Adenosine to inosine editase domain profile.	RED1_HUMAN	370-737	1	- B:370-697

Asymmetric Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.13c	ENST00000360697	13c	ENSE00001507135	chr21:46591557-46591599	43	RED1_HUMAN	1-10	10	0	-	-
1.14b	ENST00000360697	14b	ENSE00001050989	chr21:46595645-46596579	935	RED1_HUMAN	10-321	312	2	A:306-321 B:306-321 (gaps)	16 16
1.16	ENST00000360697	16	ENSE00001608449	chr21:46600245-46600359	115	RED1_HUMAN	322-360	39	2	A:322-360 B:322-360	39 39
1.17	ENST00000360697	17	ENSE00001050991	chr21:46602500-46602668	169	RED1_HUMAN	360-416	57	2	A:360-416 B:360-416	57 57
1.18	ENST00000360697	18	ENSE00001050987	chr21:46603277-46603425	149	RED1_HUMAN	416-466	51	2	A:416-457 B:416-461	42 46
1.19	ENST00000360697	19	ENSE00001507134	chr21:46604389-46604508	120	RED1_HUMAN	466-506	41	0	-	-
1.20	ENST00000360697	20	ENSE00001050983	chr21:46604838-46605006	169	RED1_HUMAN	506-562	57	2	A:475-522 B:474-522 (gaps)	48 49
1.21	ENST00000360697	21	ENSE00001507133	chr21:46624470-46624651	182	RED1_HUMAN	562-623	62	2	A:522-583 B:522-583	62 62
1.22	ENST00000360697	22	ENSE00000897018	chr21:46640751-46640929	179	RED1_HUMAN	623-682	60	2	A:583-642 B:583-642	60 60
1.23c	ENST00000360697	23c	ENSE00001530203	chr21:46641933-46646475	4543	RED1_HUMAN	683-741	59	2	A:643-700 B:643-700	58 58

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:378
 aligned with RED1_HUMAN | P78563 from UniProtKB/Swiss-Prot  Length:741

    Alignment length:435
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735     
           RED1_HUMAN   306 SRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHEPILEGSRSYTQAGVQWCNHGSLQPRPPGLLSDPSTSTFQGAGTTEPADRHPNRKARGQLRTKIESGEGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLT 740
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhh....hhhhh...eeeeeeee..hhhhheeeeeee.....hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.....eee...eeeeeee.....hhhhhh---------------------------------------------------------......eeee......ee........hhhhhhh....eeehhhhhhhhhhhhh.hhhhhhh......eeeeee....hhhhhhhhhhhhhh..............eeee..............eeeeee......eeee....ee........hhhhhhhhhhhhhh..hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------A_DEAMIN_EDITASE  PDB: A:370-697 UniProt: 370-737                                                                                                                                                                                                                                                                                                                               --- PROSITE
           Transcript 1 (1) Exon 1.14b      Exon 1.16  PDB: A:322-360              -------------------------------------------------------Exon 1.18  PDB: A:416-457 UniProt: 416-466         ---------------------------------------Exon 1.20  PDB: A:475-522 UniProt: 506-562 [INCOMPLETE]  ------------------------------------------------------------Exon 1.22  PDB: A:583-642 UniProt: 623-682                  Exon 1.23c  PDB: A:643-700 UniProt: 683-741 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.17  PDB: A:360-416 UniProt: 360-416               -------------------------------------------------Exon 1.19  PDB: - UniProt: 466-506       -------------------------------------------------------Exon 1.21  PDB: A:522-583 UniProt: 562-623                    --------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1zy7 A 306 SRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIF---------------------------------------------------------KARGQLRTKIESGEGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLT 700
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455 |       -         -         -         -         -       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695     
                                                                                                                                                                                 457                                                       475

Chain B from PDB  Type:PROTEIN  Length:362
 aligned with RED1_HUMAN | P78563 from UniProtKB/Swiss-Prot  Length:741

    Alignment length:435
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735     
           RED1_HUMAN   306 SRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHEPILEGSRSYTQAGVQWCNHGSLQPRPPGLLSDPSTSTFQGAGTTEPADRHPNRKARGQLRTKIESGEGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLT 740
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------    -----------------------------------------------------A_deamin-1zy7B01 B:370-693                                                                                                                                                                                                                                                                                                                                                  ------- Pfam domains (1)
           Pfam domains (2) -------    -----------------------------------------------------A_deamin-1zy7B02 B:370-693                                                                                                                                                                                                                                                                                                                                                  ------- Pfam domains (2)
         Sec.struct. author .......----..hhhhhhhhhhhhhhhhhhhh.....hhhhh...eeeeeee...hhhhheeeeeee.....hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.....eee....eeeeee.....hhhhh.....----------------------------------------------------.......eee......eee.-----------------....hhhhhhhhhhhhh.hhhhhhh......eeeeee....hhhhhhhhhhhhhh..............eeee..............eeeeee......eeee....ee........hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------A_DEAMIN_EDITASE  PDB: B:370-697 UniProt: 370-737                                                                                                                                                                                                                                                                                                                               --- PROSITE
           Transcript 1 (1) Exon 1.14b      Exon 1.16  PDB: B:322-360              -------------------------------------------------------Exon 1.18  PDB: B:416-461 UniProt: 416-466         ---------------------------------------Exon 1.20  PDB: B:474-522 (gaps) UniProt: 506-562        ------------------------------------------------------------Exon 1.22  PDB: B:583-642 UniProt: 623-682                  Exon 1.23c  PDB: B:643-700 UniProt: 683-741 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.17  PDB: B:360-416 UniProt: 360-416               -------------------------------------------------Exon 1.19  PDB: - UniProt: 466-506       -------------------------------------------------------Exon 1.21  PDB: B:522-583 UniProt: 562-623                    --------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1zy7 B 306 SRQPIPS----LHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHE----------------------------------------------------RKARGQLRTKIESGEGTIPV-----------------LLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLT 700
                                  |  - |     325       335       345       355       365       375       385       395       405       415       425       435       445       455     |   -         -         -         -         -       475       485       | -         -     | 515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695     
                                312  317                                                                                                                                             461                                                  474                493               511

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 '\|'

(no "SCOP Domain" information available for 1ZY7)

(no "CATH Domain" information available for 1ZY7)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CDA (39)

Family: A_deamin (1)

Homo sapiens (Human) (1)

1a	A_deamin-1zy7B01	B:370-693
1b	A_deamin-1zy7B02	B:370-693

Asymmetric Unit(hide GO term definitions)

Chain A,B (RED1_HUMAN | P78563)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004000	adenosine deaminase activity	Catalysis of the reaction: adenosine + H2O = inosine + NH3.
	GO:0003726	double-stranded RNA adenosine deaminase activity	Catalysis of the reaction: adenosine + H2O = inosine + NH3, in a double-stranded RNA molecule.
	GO:0003725	double-stranded RNA binding	Interacting selectively and non-covalently with double-stranded RNA.
	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:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	GO:0006382	adenosine to inosine editing	The conversion of an adenosine residue to inosine in an RNA molecule by deamination.
	GO:0016553	base conversion or substitution editing	Any base modification or substitution events that result in alterations in the coding potential or structural properties of RNAs as a result of changes in the base-pairing properties of the modified ribonucleoside(s).
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0030336	negative regulation of cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0044387	negative regulation of protein kinase activity by regulation of protein phosphorylation	The stopping, prevention, or reduction in frequency, rate or extent of protein kinase activity as a result of regulating the phosphorylation status of that protein kinase.
	GO:0045070	positive regulation of viral genome replication	Any process that activates or increases the frequency, rate or extent of viral genome replication.
	GO:0051726	regulation of cell cycle	Any process that modulates the rate or extent of progression through the cell cycle.
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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

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		Pro B:592 - Gly B:593	[ RasMol ]

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	1zy7
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	RED1_HUMAN \| P78563	:	5ed1 5ed2 5hp2 5hp3

(no "Related Entries Specified in the PDB File" available for 1ZY7)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (8, 16)

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