3BTN - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ANTIZYME INHIBITOR, AN ORNITHINE DECARBOXYLASE HOMOLOGOUS PROTEIN

Authors :   O. Dym, T. Unger, S. Albeck, C. Kahana, Israel Structural Proteomics Center (Ispc)

Date :   30 Dec 07 (Deposition) - 15 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Tim-Like A/B Barrel Domain And A Sheet Domain, Structural Genomics, Israel Structural Proteomics Center, Ispc, Polyamine Biosynthesis, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Albeck, O. Dym, T. Unger, Z. Snapir, Z. Bercovich, C. Kahana
Crystallographic And Biochemical Studies Revealing The Structural Basis For Antizyme Inhibitor Function.
Protein Sci. V. 17 793 2008
PubMed-ID: 18369191 | Reference-DOI: 10.1110/PS.073427208
(for further references see the PDB file header)

Molecule 1 - ANTIZYME INHIBITOR 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PETG-20A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	AZIN1, OAZI, OAZIN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	AZI, ORNITHINE DECARBOXYLASE ANTIZYME INHIBITOR

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3BTN)

(no "Site" information available for 3BTN)

(no "SS Bond" information available for 3BTN)

(no "Cis Peptide Bond" information available for 3BTN)

(no "SAP(SNP)/Variant" information available for 3BTN)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ODR_DC_2_2	PS00879	Orn/DAP/Arg decarboxylases family 2 signature 2.	AZIN1_MOUSE	222-239	2	A:222-239 B:222-239

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ODR_DC_2_2	PS00879	Orn/DAP/Arg decarboxylases family 2 signature 2.	AZIN1_MOUSE	222-239	1	A:222-239 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ODR_DC_2_2	PS00879	Orn/DAP/Arg decarboxylases family 2 signature 2.	AZIN1_MOUSE	222-239	1	- B:222-239

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ODR_DC_2_2	PS00879	Orn/DAP/Arg decarboxylases family 2 signature 2.	AZIN1_MOUSE	222-239	2	A:222-239 B:222-239

Asymmetric Unit (10, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENSMUST00000110329	1b	ENSMUSE00000683549	chr15:38449018-38448664	355	AZIN1_MOUSE	-	0	0	-	-
1.4a	ENSMUST00000110329	4a	ENSMUSE00000361050	chr15:38444364-38444228	137	AZIN1_MOUSE	-	0	0	-	-
1.5	ENSMUST00000110329	5	ENSMUSE00000683548	chr15:38437101-38436942	160	AZIN1_MOUSE	-	0	0	-	-
1.6	ENSMUST00000110329	6	ENSMUSE00000412170	chr15:38431355-38431159	197	AZIN1_MOUSE	1-34	34	2	A:8-34 B:8-34	27 27
1.7b	ENSMUST00000110329	7b	ENSMUSE00000231222	chr15:38430226-38430053	174	AZIN1_MOUSE	35-92	58	2	A:35-92 B:35-92	58 58
1.8	ENSMUST00000110329	8	ENSMUSE00000897288	chr15:38428596-38428424	173	AZIN1_MOUSE	93-150	58	2	A:93-150 B:93-150	58 58
1.9b	ENSMUST00000110329	9b	ENSMUSE00000231211	chr15:38427153-38427019	135	AZIN1_MOUSE	150-195	46	2	A:150-195 (gaps) B:150-195 (gaps)	46 46
1.10	ENSMUST00000110329	10	ENSMUSE00000231204	chr15:38425109-38425028	82	AZIN1_MOUSE	195-222	28	2	A:195-222 B:195-222	28 28
1.11	ENSMUST00000110329	11	ENSMUSE00000231198	chr15:38424121-38424047	75	AZIN1_MOUSE	223-247	25	2	A:223-247 B:223-247	25 25
1.12a	ENSMUST00000110329	12a	ENSMUSE00000231192	chr15:38423391-38423229	163	AZIN1_MOUSE	248-302	55	2	A:248-293 B:248-292	46 45
1.13a	ENSMUST00000110329	13a	ENSMUSE00000231187	chr15:38422114-38421999	116	AZIN1_MOUSE	302-340	39	2	A:311-340 (gaps) B:311-340 (gaps)	30 30
1.14b	ENSMUST00000110329	14b	ENSMUSE00000231179	chr15:38421445-38421231	215	AZIN1_MOUSE	341-412	72	2	A:341-412 (gaps) B:347-412	72 66
1.15b	ENSMUST00000110329	15b	ENSMUSE00000683547	chr15:38420227-38417993	2235	AZIN1_MOUSE	412-448	37	2	A:412-435 B:412-434	24 23

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:394
 aligned with AZIN1_MOUSE | O35484 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:428
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427        
          AZIN1_MOUSE     8 ANYSVGLLDEGTNLGNVIDNYVYEHTLTGKNAFFVGDLGKIVKKHSQWQTVVAQIKPFYTVKCNSTPAVLEILAALGTGFACSSKNEMALVQELGVSPENIIFTSPCKQVSQIKYAAKVGVNIMTCDNEIELKKIARNHPNAKVLLHIATEDNIGGEDGNMKFGTTLKNCRHLLECAKELDVQIIGVKFHVSSACKEYQVYVHALSDARCVFDMAGEFGFTMNMLDIGGGFTGTEIQLEEVNHVISPLLDIYFPEGSGIQIISEPGSYYVSSAFTLAVNIIAKKVVENDKFSSGVEKNGSDEPAFVYYMNDGVYGSFASKLSEDLNTIPEVHKKYKEDEPLFTSSLWGPSCDELDQIVESCLLPELNVGDWLIFDNMGADSFHEPSAFNDFQRPAIYFMMSFSDWYEMQDAGITSDAMMKNFFFAPSC 435
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------3btnA01    3btnA02 A:46-276 Alanine racemase                                                                                                                                                                                                      3btnA01 A:35-45,A                 :277-407 Lyase, Orn    ithine D     ecarboxylase; Chain A, domain 1                              ---------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhh..eeeeee.hhh.hhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhhh..eeee.hhhhhhhhhhhh...eeeee.....--------.....hhhhhhhhhhhhhhhh.eeeeee..........hhhhhhhhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhhhhhhhhh......eeee..hhhhhh..eeeeeeeeeee..-----------------.eeeee.......hhhhhh----...ee...-----.eeeeeee........eeeeeeeee......eeee...........hhhhh....eeeeeeehhhhhhhhhhhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ODR_DC_2_2        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:8-34      Exon 1.7b  PDB: A:35-92 UniProt: 35-92                    Exon 1.8  PDB: A:93-150 UniProt: 93-150                   --------------------------------------------Exon 1.10  PDB: A:195-222   Exon 1.11  PDB: A:223-247Exon 1.12a  PDB: A:248-293 UniProt: 248-302            --------------------------------------Exon 1.14b  PDB: A:341-412 (gaps) UniProt: 341-412                      ----------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: A:150-195 (gaps)              ----------------------------------------------------------------------------------------------------------Exon 1.13a  PDB: A:311-340 (gaps)      -----------------------------------------------------------------------Exon 1.15b [INCOMPLETE]  Transcript 1 (2)
                 3btn A   8 ANYSVGLLDEGTNLGNVIDNYVYEHTLTGKNAFFVGDLGKIVKKHSQWQTVVAQIKPFYTVKCNSTPAVLEILAALGTGFACSSKNEMALVQELGVSPENIIFTSPCKQVSQIKYAAKVGVNIMTCDNEIELKKIARNHPNAKVLLHIATED--------MKFGTTLKNCRHLLECAKELDVQIIGVKFHVSSACKEYQVYVHALSDARCVFDMAGEFGFTMNMLDIGGGFTGTEIQLEEVNHVISPLLDIYFPEGSGIQIISEPGSYYVSSAFTLAVNIIAKKVV-----------------AFVYYMNDGVYGSFASKLS----TIPEVHKK-----PLFTSSLWGPSCDELDQIVESCLLPELNVGDWLIFDNMGADSFHEPSAFNDFQRPAIYFMMSFSDWYEMQDAGITSDAMMKNFFFAPSC 435
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157 |       -|      177       187       197       207       217       227       237       247       257       267       277       287     |   -         -   |   317       327 |    |337   |   347       357       367       377       387       397       407       417       427        
                                                                                                                                                                                 159      168                                                                                                                          293               311               329  334    341   347

Chain B from PDB  Type:PROTEIN  Length:390
 aligned with AZIN1_MOUSE | O35484 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:427
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       
          AZIN1_MOUSE     8 ANYSVGLLDEGTNLGNVIDNYVYEHTLTGKNAFFVGDLGKIVKKHSQWQTVVAQIKPFYTVKCNSTPAVLEILAALGTGFACSSKNEMALVQELGVSPENIIFTSPCKQVSQIKYAAKVGVNIMTCDNEIELKKIARNHPNAKVLLHIATEDNIGGEDGNMKFGTTLKNCRHLLECAKELDVQIIGVKFHVSSACKEYQVYVHALSDARCVFDMAGEFGFTMNMLDIGGGFTGTEIQLEEVNHVISPLLDIYFPEGSGIQIISEPGSYYVSSAFTLAVNIIAKKVVENDKFSSGVEKNGSDEPAFVYYMNDGVYGSFASKLSEDLNTIPEVHKKYKEDEPLFTSSLWGPSCDELDQIVESCLLPELNVGDWLIFDNMGADSFHEPSAFNDFQRPAIYFMMSFSDWYEMQDAGITSDAMMKNFFFAPS 434
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------3btnB01    3btnB02 B:46-276 Alanine racemase                                                                                                                                                                                                      3btnB01 B:35-45,                  B:277-407 Lyase, O     rnithin      e Decarboxylase; Chain A, domain 1                           --------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhh.eeeeee.hhh.hhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhhh..eeee.hhhhhhhhhhhh...eeeee.....--------.....hhhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhhhhhhhhh......eeee..hhhhhh..eeeeeeeeeee.------------------.eeeee.......hhhhh-----..eee..------.eeeeeee........eeeeeeeee......eeee...........hhhhh....eeeeeeehhhhhhhhhhhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ODR_DC_2_2        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: B:8-34      Exon 1.7b  PDB: B:35-92 UniProt: 35-92                    Exon 1.8  PDB: B:93-150 UniProt: 93-150                   --------------------------------------------Exon 1.10  PDB: B:195-222   Exon 1.11  PDB: B:223-247Exon 1.12a  PDB: B:248-292 UniProt: 248-302            --------------------------------------Exon 1.14b  PDB: B:347-412 UniProt: 341-412 [INCOMPLETE]                ---------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: B:150-195 (gaps)              ----------------------------------------------------------------------------------------------------------Exon 1.13a  PDB: B:311-340 (gaps)      -----------------------------------------------------------------------Exon 1.15b [INCOMPLETE] Transcript 1 (2)
                 3btn B   8 ANYSVGLLDEGTNLGNVIDNYVYEHTLTGKNAFFVGDLGKIVKKHSQWQTVVAQIKPFYTVKCNSTPAVLEILAALGTGFACSSKNEMALVQELGVSPENIIFTSPCKQVSQIKYAAKVGVNIMTCDNEIELKKIARNHPNAKVLLHIATED--------MKFGTTLKNCRHLLECAKELDVQIIGVKFHVSSACKEYQVYVHALSDARCVFDMAGEFGFTMNMLDIGGGFTGTEIQLEEVNHVISPLLDIYFPEGSGIQIISEPGSYYVSSAFTLAVNIIAKKV------------------AFVYYMNDGVYGSFASKL-----TIPEVHK------PLFTSSLWGPSCDELDQIVESCLLPELNVGDWLIFDNMGADSFHEPSAFNDFQRPAIYFMMSFSDWYEMQDAGITSDAMMKNFFFAPS 434
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157 |       -|      177       187       197       207       217       227       237       247       257       267       277       287    |    -         -   |   317       327|     |337  |    347       357       367       377       387       397       407       417       427       
                                                                                                                                                                                 159      168                                                                                                                         292                311              328   334   340    347

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 3BTN)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Alanine racemase (53)

House mouse (Mus musculus) (2)

1a	3btnA02	A:46-276
1b	3btnB02	B:46-276

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lyase, Ornithine Decarboxylase; Chain A, domain 1 (47)

Homologous Superfamily: Lyase, Ornithine Decarboxylase; Chain A, domain 1 (47)

House mouse (Mus musculus) (2)

2a	3btnA01	A:35-45,A:277-407
2b	3btnB01	B:35-45,B:277-407

(no "Pfam Domain" information available for 3BTN)

Asymmetric Unit(hide GO term definitions)

Chain A,B (AZIN1_MOUSE | O35484)

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:0042978	ornithine decarboxylase activator activity	Upregulation of the activity of the enzyme ornithine decarboxylase.
biological process
	GO:0042177	negative regulation of protein catabolic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0006596	polyamine biosynthetic process	The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.
	GO:0006595	polyamine metabolic process	The chemical reactions and pathways involving polyamines, any organic compound containing two or more amino groups.
	GO:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
	GO:1902269	positive regulation of polyamine transmembrane transport	Any process that activates or increases the frequency, rate or extent of polyamine transmembrane transport.
	GO:0033387	putrescine biosynthetic process from ornithine	The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane by decarboxylation of ornithine.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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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7odc	CRYSTAL STRUCTURE OF MOUSE ORNITHINE DECARBOXYLASE

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