1Y88 - JenaLib

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Description

Title :   CRYSTAL STRUCTURE OF PROTEIN OF UNKNOWN FUNCTION AF1548

Authors :   V. V. Lunin, E. Evdokimova, M. Kudritskaya, M. E. Cuff, A. Joachimiak, A A. Savchenko, Midwest Center For Structural Genomics (Mcsg)

Date :   10 Dec 04 (Deposition) - 21 Dec 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)
Biol. Unit 2: A  (6x)
Biol. Unit 3: A  (1x)

Keywords :   Af1548, Apc5567, Structural Genomics, Protein Structure Initiative, Psi, Midwest Center For Structural Genomics Center, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. V. Lunin, E. Evdokimova, M. Kudritskaya, M. E. Cuff, A. Joachimiak, A. Edwards, A. Savchenko
The Crystal Structure Of Hypothetical Protein Af1548 From Archaeoglobus Fulgidus
To Be Published
PubMed: search

Compounds

Molecule 1 - HYPOTHETICAL PROTEIN AF1548
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	MODIFIED PET15B
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector	:	PLASMID
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A
Biological Unit 2 (6x)	:	A
Biological Unit 3 (1x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 10)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	SO4	9	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 18)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SO4	18	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 54)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SO4	54	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 9)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SO4	9	Ligand/Ion	SULFATE ION

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:128 , CYS A:151 , ARG A:152 , HOH A:358	BINDING SITE FOR RESIDUE CL A 201
02	AC2	SOFTWARE	GLY A:62 , LEU A:63 , SER A:93 , GLU A:95 , HOH A:326 , HOH A:342	BINDING SITE FOR RESIDUE SO4 A 301
03	AC3	SOFTWARE	GLY A:62 , LEU A:63 , LYS A:64 , GLU A:65 , HOH A:326 , HOH A:404	BINDING SITE FOR RESIDUE SO4 A 302
04	AC4	SOFTWARE	VAL A:28 , GLN A:29 , HIS A:79 , GLU A:160 , HOH A:371	BINDING SITE FOR RESIDUE SO4 A 303
05	AC5	SOFTWARE	GLN A:29 , ASN A:31 , VAL A:33 , GLU A:34 , LYS A:78 , GLU A:95 , LYS A:98 , HOH A:310 , HOH A:376	BINDING SITE FOR RESIDUE SO4 A 304
06	AC6	SOFTWARE	HIS A:55 , ASN A:56 , ILE A:57	BINDING SITE FOR RESIDUE SO4 A 305
07	AC7	SOFTWARE	HIS A:18 , ARG A:43	BINDING SITE FOR RESIDUE SO4 A 306
08	AC8	SOFTWARE	ARG A:163 , SER A:168 , ALA A:169 , HOH A:355 , HOH A:399	BINDING SITE FOR RESIDUE SO4 A 307
09	AC9	SOFTWARE	ARG A:43 , ASP A:44 , LYS A:115 , LYS A:125 , ARG A:152 , HOH A:332	BINDING SITE FOR RESIDUE SO4 A 308
10	BC1	SOFTWARE	THR A:22 , LYS A:23 , THR A:24 , HOH A:321 , HOH A:452	BINDING SITE FOR RESIDUE SO4 A 309

SS Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	A:32	-	A:102

Cis Peptide Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	Tyr A:112	-	Pro A:113

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y88)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 1Y88)

Exons (0, 0)

(no "Exon" information available for 1Y88)

Sequences/Alignments

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:184
 aligned with Y1548_ARCFU | O28724 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:184
                                    1                                                                                                                                                                          174  
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 |  
          Y1548_ARCFU     - --------MARLLEEHGFETKTNVIVQGNCVEQEIDVVAERDGERYMIECKFHNIPVYTGLKEAMYTYARFLDVEKHGFTQPWIFTNTKFSEEAKKYAGCVGIKLTGWSYPEKEGIEVLLESKGLYPITILRIDKEVLDELVRAGLVFCRDVVSAGEEKLREIGLSAKKAREVIAEAKKVIG--   -
               SCOP domains d1y88a2 A:3-127 Hypothetical protein AF1548, N-terminal domain                                                               d1y88a1 A:128-186                                           SCOP domains
               CATH domains 1y88A01 A:3-127  [code=3.40.1350.10, no name defined]                                                                        1y88A02 A:128-186                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh...eeeeeeeee....eeeeeeeeee..eeeeeee.......eehhhhhhhhhhhhhhhhhhh..eeeee...eehhhhhhhhhhhh.eee........hhhhhhhh....hhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y88 A   3 NLYFQGHMVARLLEEHGFETKTNVIVQGNCVEQEIDVVAERDGERYMIECKFHNIPVYTGLKEAMYTYARFLDVEKHGFTQPWIFTNTKFSEEAKKYAGCVGIKLTGWSYPEKEGIEVLLESKGLYPITILRIDKEVLDELVRAGLVFCRDVVSAGEEKLREIGLSAKKAREVIAEAKKVIGGS 186
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: SAM domain-like (639)

Superfamily: Rad51 N-terminal domain-like (25)

Family: Hypothetical protein AF1548, C-terminal domain (1)

Protein domain: Hypothetical protein AF1548, C-terminal domain (1)

Archaeoglobus fulgidus [TaxId: 2234] (1)

d1y88a1

A:128-186

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

Fold: Restriction endonuclease-like (209)

Superfamily: Restriction endonuclease-like (170)

Family: MRR-like (1)

Protein domain: Hypothetical protein AF1548, N-terminal domain (1)

Archaeoglobus fulgidus [TaxId: 2234] (1)

d1y88a2

A:3-127

CATH Domains (2, 2)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Trna Endonuclease; Chain: A, domain 1 (24)

Homologous Superfamily: [code=3.40.1350.10, no name defined] (24)

Archaeoglobus fulgidus. Organism_taxid: 2234. (1)

1y88A01

A:3-127

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: 5' to 3' exonuclease, C-terminal subdomain (384)

Archaeoglobus fulgidus. Organism_taxid: 2234. (1)

1y88A02

A:128-186

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 1Y88)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (Y1548_ARCFU | O28724)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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:0009307	DNA restriction-modification system	A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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	1y88
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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Exons (0, 0)

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