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Title :   CRYSTAL STRUCTURE OF AF2198, A JAB1/MPN DOMAIN PROTEIN FROM ARCHAEOGLOBUS FULGIDUS

Authors :   H. J. T. T. Tran, M. D. Allen, J. Lowe, M. Bycroft

Date :   04 Jun 03 (Deposition) - 14 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Proteasome, Deubiquitination, Archaea, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. J. T. T. Tran, M. D. Allen, J. Lowe, M. Bycroft
The Structure Of The Jab1/Mpn Domain And Its Implications For Proteasome Function
Biochemistry V. 42 11460 2003
PubMed-ID: 14516197 | Reference-DOI: 10.1021/BI035033G

Molecule 1 - HYPOTHETICAL PROTEIN AF2198
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	C41
	Expression System Taxid	:	562
	Expression System Vector	:	PRSETA
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234
	Synonym	:	AF2198

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	144	2	Ligand/Ion	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	144	1	Ligand/Ion	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	144	-1	Ligand/Ion	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	144	-1	Ligand/Ion	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	144	1	Ligand/Ion	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:70 , HIS A:72 , ASP A:83 , 144 A:1123	BINDING SITE FOR RESIDUE ZN A1122
2	AC2	SOFTWARE	HIS B:70 , HIS B:72 , ASP B:83 , HOH B:2070 , HOH B:2071	BINDING SITE FOR RESIDUE ZN B1123
3	AC3	SOFTWARE	HIS C:70 , HIS C:72 , ASP C:83 , HOH C:2078 , ARG D:89	BINDING SITE FOR RESIDUE ZN C1123
4	AC4	SOFTWARE	HIS D:70 , HIS D:72 , ASP D:83 , 144 D:1124	BINDING SITE FOR RESIDUE ZN D1123
5	AC5	SOFTWARE	GLU A:25 , HIS A:70 , HIS A:72 , SER A:80 , GLU A:82 , ASP A:83 , ZN A:1122 , HOH A:2065 , ARG B:89	BINDING SITE FOR RESIDUE 144 A1123
6	AC6	SOFTWARE	ARG C:89 , GLU D:25 , HIS D:70 , HIS D:72 , SER D:80 , GLU D:82 , ASP D:83 , ZN D:1123	BINDING SITE FOR RESIDUE 144 D1124

Asymmetric Unit

No.	Residues
1	A:77	-	A:98
2	B:77	-	B:98
3	C:77	-	C:98
4	D:77	-	D:98

Asymmetric Unit

No.	Residues
1	His A:22	-	Pro A:23
2	Tyr A:99	-	Pro A:100
3	His B:22	-	Pro B:23
4	Tyr B:99	-	Pro B:100
5	His C:22	-	Pro C:23
6	Tyr C:99	-	Pro C:100
7	His D:22	-	Pro D:23
8	Tyr D:99	-	Pro D:100

(no "SAP(SNP)/Variant" information available for 1OI0)

(no "PROSITE Motif" information available for 1OI0)

(no "Exon" information available for 1OI0)

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:108
 aligned with O28085_ARCFU | O28085 from UniProtKB/TrEMBL  Length:121

    Alignment length:121
                               1                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117 
         O28085_ARCFU     - ---MKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPFVSGSVSAVIHLDMLPIGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVV 118
               SCOP domains d1oi0a_ A: Hypothetical protein AF2198                                                                                    SCOP domains
               CATH domains 1oi0A00 A:1-121 Cytidine Deaminase, domain 2                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeehhhhhhhhhhhhhhh....eeeeee...ee.eeee.....-------------...eeeeeeeee.......hhhhhhhhhhh..eeeeee.......eeeee....ee..eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi0 A   1 GSSMKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPFVS-------------IGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVV 121
                                    10        20        30        40      |  -         -|       70        80        90       100       110       120 
                                                                         47            61

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with O28085_ARCFU | O28085 from UniProtKB/TrEMBL  Length:121

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         O28085_ARCFU     1 MKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPFVSGSVSAVIHLDMLPIGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVVE 119
               SCOP domains d1oi0b_ B: Hypothetical protein AF2198                                                                                  SCOP domains
               CATH domains 1oi0B00 B:4-122 Cytidine Deaminase, domain              2                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhh....eeeeeee..eeeeeee...-------------.....eeeeeeeee.......hhhhhhhhhhh..eeeeee.......eeee.........eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi0 B   4 MKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPF-------------LPIGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVVE 122
                                    13        23        33        43 |       -     |  63        73        83        93       103       113         
                                                                    45            59

Chain C from PDB  Type:PROTEIN  Length:104
 aligned with O28085_ARCFU | O28085 from UniProtKB/TrEMBL  Length:121

    Alignment length:122
                               1                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117  
         O28085_ARCFU     - ---MKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPFVSGSVSAVIHLDMLPIGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVVE 119
               SCOP domains d1oi0c_ C: Hypothetical protein AF2198                                                                                     SCOP domains
               CATH domains 1oi0C00 C:1-122 Cytidine Deaminase, domain                   2                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeehhhhhhhhhhhhhhh....eeeeee...ee.eeee.------------------..eeeeeeeee.......hhhhhhhhhhh..eeeeee.......eeee.....ee..eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi0 C   1 GSSMKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFL------------------GMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVVE 122
                                    10        20        30        40  |      -         - |      70        80        90       100       110       120  
                                                                     43                 62

Chain D from PDB  Type:PROTEIN  Length:108
 aligned with O28085_ARCFU | O28085 from UniProtKB/TrEMBL  Length:121

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         O28085_ARCFU     1 MKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPFVSGSVSAVIHLDMLPIGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVVE 119
               SCOP domains d1oi0d_ D: Hypothetical protein AF2198                                                                                  SCOP domains
               CATH domains 1oi0D00 D:4-122 Cytidine Deaminase, domain 2                                                                            CATH domains
           Pfam domains (1) ---Prok-JAB-1oi0D01 D:7-109                                                                               ------------- Pfam domains (1)
           Pfam domains (2) ---Prok-JAB-1oi0D02 D:7-109                                                                               ------------- Pfam domains (2)
           Pfam domains (3) ---Prok-JAB-1oi0D03 D:7-109                                                                               ------------- Pfam domains (3)
           Pfam domains (4) ---Prok-JAB-1oi0D04 D:7-109                                                                               ------------- Pfam domains (4)
         Sec.struct. author .eeehhhhhhhhhhhhhhh....eeeeeee..eeeeeee......-----------....eeeeeeeee.......hhhhhhhhh....eeeeee.......eeee.........eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi0 D   4 MKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPFVSG-----------PIGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVVE 122
                                    13        23        33        43    |    -      | 63        73        83        93       103       113         
                                                                       48          60

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: Alpha and beta proteins (a/b) (23833)

Fold: Cytidine deaminase-like (78)

Superfamily: JAB1/MPN domain (2)

Family: JAB1/MPN domain (2)

Protein domain: Hypothetical protein AF2198 (2)

Archaeoglobus fulgidus [TaxId: 2234] (2)

1a	d1oi0a_	A:
1b	d1oi0b_	B:
1c	d1oi0c_	C:
1d	d1oi0d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Cytidine Deaminase; domain 2 (44)

Homologous Superfamily: Cytidine Deaminase, domain 2 (32)

Archaeoglobus fulgidus. Organism_taxid: 2234. (1)

1a	1oi0A00	A:1-121
1b	1oi0D00	D:4-122
1c	1oi0B00	B:4-122
1d	1oi0C00	C:1-122

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: JAB (8)

Family: Prok-JAB (3)

Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (2)

1a	Prok-JAB-1oi0D01	D:7-109
1b	Prok-JAB-1oi0D02	D:7-109
1c	Prok-JAB-1oi0D03	D:7-109
1d	Prok-JAB-1oi0D04	D:7-109

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (O28085_ARCFU | O28085)

molecular function
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

Asymmetric Unit
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		His D:22 - Pro D:23	[ RasMol ]
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		Tyr B:99 - Pro B:100	[ RasMol ]
		Tyr C:99 - Pro C:100	[ RasMol ]
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Description

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Ligands, Modified Residues, Ions (2, 6)

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SS Bonds (4, 4)

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