1F5M - JenaLib

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Title :   STRUCTURE OF THE GAF DOMAIN

Authors :   Y. S. Ho, L. M. Burden, J. H. Hurley

Date :   15 Jun 00 (Deposition) - 10 Nov 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Gaf, Cgmp Binding, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. S. Ho, L. M. Burden, J. H. Hurley
Structure Of The Gaf Domain, A Ubiquitous Signaling Motif And A New Class Of Cyclic Gmp Receptor.
Embo J. V. 19 5288 2000
PubMed-ID: 11032796 | Reference-DOI: 10.1093/EMBOJ/19.20.5288
(for further references see the PDB file header)

Molecule 1 - GAF
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PGEX
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 9)

No.	Name	Count	Type	Full Name
1	BR	9	Ligand/Ion	BROMIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:163 , HOH A:646	BINDING SITE FOR RESIDUE BR A 501
2	AC2	SOFTWARE	SER B:16	BINDING SITE FOR RESIDUE BR B 502
3	AC3	SOFTWARE	GLN A:95 , HOH A:644	BINDING SITE FOR RESIDUE BR A 503
4	AC4	SOFTWARE	GLN B:95	BINDING SITE FOR RESIDUE BR B 504
5	AC5	SOFTWARE	LYS A:171 , ASN A:174 , LYS A:175 , HOH A:516	BINDING SITE FOR RESIDUE BR A 505
6	AC6	SOFTWARE	GLU B:156 , HOH B:518	BINDING SITE FOR RESIDUE BR B 506
7	AC7	SOFTWARE	LYS A:143 , THR A:144 , HOH A:605	BINDING SITE FOR RESIDUE BR A 507
8	AC8	SOFTWARE	LYS B:21 , GLU B:22 , HOH B:570	BINDING SITE FOR RESIDUE BR B 508
9	AC9	SOFTWARE	HOH B:569	BINDING SITE FOR RESIDUE BR B 509

Asymmetric Unit

No.	Residues
1	A:91	-	A:125
2	B:91	-	B:125

(no "Cis Peptide Bond" information available for 1F5M)

(no "SAP(SNP)/Variant" information available for 1F5M)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0067	PS01320	Uncharacterized protein family UPF0067 signature.	FRMSR_YEAST	115-132	2	A:115-132 B:115-132

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0067	PS01320	Uncharacterized protein family UPF0067 signature.	FRMSR_YEAST	115-132	2	A:115-132 B:115-132

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0067	PS01320	Uncharacterized protein family UPF0067 signature.	FRMSR_YEAST	115-132	4	A:115-132 B:115-132

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0067	PS01320	Uncharacterized protein family UPF0067 signature.	FRMSR_YEAST	115-132	4	A:115-132 B:115-132

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YKL069W	1	YKL069W.1	XI:306929-307471	543	FRMSR_YEAST	1-180	180	2	A:4-179 B:3-179	176 177

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:176
 aligned with FRMSR_YEAST | P36088 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:176
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      
          FRMSR_YEAST     4 STGFHHADHVNYSSNLNKEEILEQLLLSYEGLSDGQVNWVCNLSNASSLIWHAYKSLAVDINWAGFYVTQASEENTLILGPFQGKVACQMIQFGKGVCGTAASTKETQIVPDVNKYPGHIACDGETKSEIVVPIISNDGKTLGVIDIDCLDYEGFDHVDKEFLEKLAKLINKSCVF 179
               SCOP domains d1f5ma_ A: Hypothetical protein ykl069wp                                                                                                                                         SCOP domains
               CATH domains 1f5mA00 A:4-179  [code=3.30.450.40, no name defined]                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...eeeeeeeee......eeeeeeeee.....eee..hhhhhhhhhhh..eee.hhhhh...........eeeeeeee.....eeeeeeeee......hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------UPF0067           ----------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:4-179 UniProt: 1-180 [INCOMPLETE]                                                                                                                               Transcript 1
                 1f5m A   4 STGFHHADHVNYSSNLNKEEILEQLLLSYEGLSDGQVNWVCNLSNASSLIWHAYKSLAVDINWAGFYVTQASEENTLILGPFQGKVACQMIQFGKGVCGTAASTKETQIVPDVNKYPGHIACDGETKSEIVVPIISNDGKTLGVIDIDCLDYEGFDHVDKEFLEKLAKLINKSCVF 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

Chain B from PDB  Type:PROTEIN  Length:177
 aligned with FRMSR_YEAST | P36088 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:177
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       
          FRMSR_YEAST     3 SSTGFHHADHVNYSSNLNKEEILEQLLLSYEGLSDGQVNWVCNLSNASSLIWHAYKSLAVDINWAGFYVTQASEENTLILGPFQGKVACQMIQFGKGVCGTAASTKETQIVPDVNKYPGHIACDGETKSEIVVPIISNDGKTLGVIDIDCLDYEGFDHVDKEFLEKLAKLINKSCVF 179
               SCOP domains d1f5mb_ B: Hypothetical protein ykl069wp                                                                                                                                          SCOP domains
               CATH domains 1f5mB00 B:3-179  [code=3.30.450.40, no name defined]                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...eeeeeeeee......eeeeeeeee.....eee..hhhhhhhhhhh..eee.hhhhh...........eeeeeeee.....eeeeeeeee......hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------UPF0067           ----------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-179 UniProt: 1-180 [INCOMPLETE]                                                                                                                                Transcript 1
                 1f5m B   3 SSTGFHHADHVNYSSNLNKEEILEQLLLSYEGLSDGQVNWVCNLSNASSLIWHAYKSLAVDINWAGFYVTQASEENTLILGPFQGKVACQMIQFGKGVCGTAASTKETQIVPDVNKYPGHIACDGETKSEIVVPIISNDGKTLGVIDIDCLDYEGFDHVDKEFLEKLAKLINKSCVF 179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Profilin-like (304)

Superfamily: GAF domain-like (54)

Family: GAF domain (24)

Protein domain: Hypothetical protein ykl069wp (2)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d1f5ma_	A:
1b	d1f5mb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Beta-Lactamase (202)

Homologous Superfamily: [code=3.30.450.40, no name defined] (27)

Baker's yeast (Saccharomyces cerevisiae) (1)

1a	1f5mA00	A:4-179
1b	1f5mB00	B:3-179

(no "Pfam Domain" information available for 1F5M)

Asymmetric Unit(hide GO term definitions)

Chain A,B (FRMSR_YEAST | P36088)

molecular function
	GO:0033745	L-methionine-(R)-S-oxide reductase activity	Catalysis of the reaction: L-methionine + thioredoxin disulfide + H2O = L-methionine (R)-S-oxide + thioredoxin.
	GO:0070191	methionine-R-sulfoxide reductase activity	Catalysis of the reaction: L-methionine R-oxide + thioredoxin = L-methionine + thioredoxin disulfide; can act on free oxidized methionine with specificity for the R enantiomer; does not act on oxidized methionine in peptide linkage. Thioredoxin disulfide is the oxidized form of thioredoxin.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0034599	cellular response to oxidative stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
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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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 9)

Sites (9, 9)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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