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Title :   THE APOBEC2 CRYSTAL STRUCTURE AND FUNCTIONAL IMPLICATIONS FOR AID

Authors :   C. Prochnow, R. Bransteitter, M. Klein, M. Goodman, X. Chen

Date :   21 Nov 06 (Deposition) - 09 Jan 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Cytidine Deaminase, Zinc-Ion Binding, Apobec, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Prochnow, R. Bransteitter, M. G. Klein, M. F. Goodman, X. S. Chen
The Apobec-2 Crystal Structure And Functional Implications For The Deaminase Aid.
Nature V. 445 447 2007
PubMed-ID: 17187054 | Reference-DOI: 10.1038/NATURE05492
(for further references see the PDB file header)

Molecule 1 - PROBABLE C->U-EDITING ENZYME APOBEC-2
	Chains	:	A, B, C, D
	EC Number	:	3.5.4.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-KG
	Expression System Strain	:	XA-90
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	APOBEC2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:60 , HIS A:98 , CYS A:128 , CYS A:131	BINDING SITE FOR RESIDUE ZN A 2000
2	AC2	SOFTWARE	HIS B:98 , CYS B:128 , CYS B:131	BINDING SITE FOR RESIDUE ZN B 2001
3	AC3	SOFTWARE	GLU C:60 , HIS C:98 , CYS C:128 , CYS C:131	BINDING SITE FOR RESIDUE ZN C 2002
4	AC4	SOFTWARE	HIS D:98 , CYS D:128 , CYS D:131	BINDING SITE FOR RESIDUE ZN D 2003

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

(no "Cis Peptide Bond" information available for 2NYT)

Asymmetric/Biological Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024406	I	136	T	ABEC2_HUMAN	Polymorphism	2076472	A/B/C/D	I	136	T

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	ABEC2_HUMAN	64-169	4	A:64-169 B:64-169 C:64-169 D:64-169

Asymmetric/Biological Unit (2, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000244669	1b	ENSE00000849850	chr6:41021043-41021217	175	ABEC2_HUMAN	1-44	44	4	A:36-44 (gaps) B:35-44 (gaps) C:40-44 D:40-44	30 31 5 5
1.2b	ENST00000244669	2b	ENSE00000849851	chr6:41029067-41029631	565	ABEC2_HUMAN	44-224	181	4	A:44-224 (gaps) B:44-224 C:44-224 D:44-224 (gaps)	181 181 181 181
1.3	ENST00000244669	3	ENSE00000849852	chr6:41031840-41032250	411	ABEC2_HUMAN	-	0	0	-	-

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
	(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:185
 aligned with ABEC2_HUMAN | Q9Y235 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:210
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224
          ABEC2_HUMAN    15 SQNGEDLENLDDPEKLKELIELPPFEIVTGERLPANFFKFQFRNVEYSSGRNKTFLCYVVEAQGKGGQVQASRGYLEDEHAAAHAEEAFFNTILPAFDPALRYNVTWYVSSSPCAACADRIIKTLSKTKNLRLLILVGRLFMWEEPEIQAALKKLKEAGCKLRIMKPQDFEYVWQNFVEQEEGESKAFQPWEDIQENFLYYEEKLADILK 224
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....---------------------.......hhhhhhhh.............eeeeeeeeee.....eeeeeeeeee.....hhhhhhhhhh........eeeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeee.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh....----......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------T---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------CYT_DCMP_DEAMINASES_2  PDB: A:64-169 UniProt: 64-169                                                      ------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:36-44 (gaps)------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.2b  PDB: A:44-224 (gaps) UniProt: 44-224                                                                                                                                       Transcript 1 (2)
                 2nyt A  36 SGGG---------------------MIVTGERLPANFFKFQFRNVEYSSGRNKTFLCYVVEAQGKGGQVQASRGYLEDEHAAAHAEEAFFNTILPAFDPALRYNVTWYVSSSPCAACADRIIKTLSKTKNLRLLILVGRLFMWEEPEIQAALKKLKEAGCKLRIMKPQDFEYVWQNFVEQEE----AFQPWEDIQENFLYYEEKLADILK 224
                               |     -         -     |  44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 |    |204       214       224
                              39                    40                                                                                                                                                         196  201

Chain B from PDB  Type:PROTEIN  Length:190
 aligned with ABEC2_HUMAN | Q9Y235 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:211
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
          ABEC2_HUMAN    14 ASQNGEDLENLDDPEKLKELIELPPFEIVTGERLPANFFKFQFRNVEYSSGRNKTFLCYVVEAQGKGGQVQASRGYLEDEHAAAHAEEAFFNTILPAFDPALRYNVTWYVSSSPCAACADRIIKTLSKTKNLRLLILVGRLFMWEEPEIQAALKKLKEAGCKLRIMKPQDFEYVWQNFVEQEEGESKAFQPWEDIQENFLYYEEKLADILK 224
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....---------------------.......hhhhhh......eeee..eeeeeeeeeeeee.....eeeeeeeeeeeee..hhhhhhhhhh........eeeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeee.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------T---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------CYT_DCMP_DEAMINASES_2  PDB: B:64-169 UniProt: 64-169                                                      ------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: B:35-44 (gaps) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.2b  PDB: B:44-224 UniProt: 44-224                                                                                                                                              Transcript 1 (2)
                 2nyt B  35 GSGGG---------------------MIVTGERLPANFFKFQFRNVEYSSGRNKTFLCYVVEAQGKGGQVQASRGYLEDEHAAAHAEEAFFNTILPAFDPALRYNVTWYVSSSPCAACADRIIKTLSKTKNLRLLILVGRLFMWEEPEIQAALKKLKEAGCKLRIMKPQDFEYVWQNFVEQEEGESKAFQPWEDIQENFLYYEEKLADILK 224
                                |    -         -      | 43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
                               39                    40

Chain C from PDB  Type:PROTEIN  Length:185
 aligned with ABEC2_HUMAN | Q9Y235 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:185
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
          ABEC2_HUMAN    40 EIVTGERLPANFFKFQFRNVEYSSGRNKTFLCYVVEAQGKGGQVQASRGYLEDEHAAAHAEEAFFNTILPAFDPALRYNVTWYVSSSPCAACADRIIKTLSKTKNLRLLILVGRLFMWEEPEIQAALKKLKEAGCKLRIMKPQDFEYVWQNFVEQEEGESKAFQPWEDIQENFLYYEEKLADILK 224
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh.............eeeeeeeeee.....eeeeeeeeee.....hhhhhhhhhh........eeeeeeeeee..hhhhhhhhhhhhh....eeeeeeeee.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------T---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------CYT_DCMP_DEAMINASES_2  PDB: C:64-169 UniProt: 64-169                                                      ------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1b ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.2b  PDB: C:44-224 UniProt: 44-224                                                                                                                                              Transcript 1 (2)
                 2nyt C  40 MIVTGERLPANFFKFQFRNVEYSSGRNKTFLCYVVEAQGKGGQVQASRGYLEDEHAAAHAEEAFFNTILPAFDPALRYNVTWYVSSSPCAACADRIIKTLSKTKNLRLLILVGRLFMWEEPEIQAALKKLKEAGCKLRIMKPQDFEYVWQNFVEQEEGESKAFQPWEDIQENFLYYEEKLADILK 224
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219

Chain D from PDB  Type:PROTEIN  Length:179
 aligned with ABEC2_HUMAN | Q9Y235 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:185
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
          ABEC2_HUMAN    40 EIVTGERLPANFFKFQFRNVEYSSGRNKTFLCYVVEAQGKGGQVQASRGYLEDEHAAAHAEEAFFNTILPAFDPALRYNVTWYVSSSPCAACADRIIKTLSKTKNLRLLILVGRLFMWEEPEIQAALKKLKEAGCKLRIMKPQDFEYVWQNFVEQEEGESKAFQPWEDIQENFLYYEEKLADILK 224
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------APOBEC_C-2nytD01 D:159-216                                -------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------APOBEC_C-2nytD02 D:159-216                                -------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------APOBEC_C-2nytD03 D:159-216                                -------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------APOBEC_C-2nytD04 D:159-216                                -------- Pfam domains (4)
         Sec.struct. author .......hhhhhh......eeee..eeeeeeeeeeeee.....eeeeeeeeeeeee..hhhhhhhhhh........eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh....------.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------T---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------CYT_DCMP_DEAMINASES_2  PDB: D:64-169 UniProt: 64-169                                                      ------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1b ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.2b  PDB: D:44-224 (gaps) UniProt: 44-224                                                                                                                                       Transcript 1 (2)
                 2nyt D  40 MIVTGERLPANFFKFQFRNVEYSSGRNKTFLCYVVEAQGKGGQVQASRGYLEDEHAAAHAEEAFFNTILPAFDPALRYNVTWYVSSSPCAACADRIIKTLSKTKNLRLLILVGRLFMWEEPEIQAALKKLKEAGCKLRIMKPQDFEYVWQNFVEQE------FQPWEDIQENFLYYEEKLADILK 224
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189     |   -  |    209       219     
                                                                                                                                                                                     195    202

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 2NYT)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CDA (39)

Family: APOBEC_C (1)

Homo sapiens (Human) (1)

1a	APOBEC_C-2nytD01	D:159-216
1b	APOBEC_C-2nytD02	D:159-216
1c	APOBEC_C-2nytD03	D:159-216
1d	APOBEC_C-2nytD04	D:159-216

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (ABEC2_HUMAN | Q9Y235)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0004126	cytidine deaminase activity	Catalysis of the reaction: cytidine + H2O = uridine + NH3.
	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:0016814	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines	Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amidine, a compound of the form R-C(=NH)-NH2.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0080111	DNA demethylation	The removal of a methyl group from one or more nucleotides within an DNA molecule.
	GO:0009972	cytidine deamination	The removal of amino group in the presence of water.
	GO:0016556	mRNA modification	The covalent alteration of one or more nucleotides within an mRNA molecule to produce an mRNA molecule with a sequence that differs from that coded genetically.
	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.

Asymmetric/Biological Unit
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Description

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