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Title :   X-RAY STRUCTURE OF PEPTIDE DEFORMYLASE FROM ARABIDOPSIS THALIANA (ATPDF1A); CRYSTALS GROWN IN PEG-6000

Authors :   S. Fieulaine, C. Juillan-Binard, A. Serero, F. Dardel, C. Giglione, T. Meinnel, J. -L. Ferrer

Date :   09 Jun 05 (Deposition) - 27 Sep 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Peptide Deformylase; Pdf1A; Eukaryote; Higher Plant; Arabidopsis Thaliana; Zinc Ion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Fieulaine, C. Juillan-Binard, A. Serero, F. Dardel, C. Giglione, T. Meinnel, J. -L. Ferrer
The Crystal Structure Of Mitochondrial (Type 1A) Peptide Deformylase Provides Clear Guidelines For The Design Of Inhibitors Specific For The Bacterial Forms
J. Biol. Chem. V. 280 42315 2005
PubMed-ID: 16192279 | Reference-DOI: 10.1074/JBC.M507155200
(for further references see the PDB file header)

Molecule 1 - PEPTIDE DEFORMYLASE, MITOCHONDRIAL
	Chains	:	A, B
	EC Number	:	3.5.1.88
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PQE30 DERIVATIVE
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	MATURE PROTEIN
	Gene	:	PDF1A
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	PDF; POLYPEPTIDE DEFORMYLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:54 , CYS A:111 , HIS A:153 , HIS A:157 , HOH A:199	BINDING SITE FOR RESIDUE ZN A 198
2	AC2	SOFTWARE	GLN B:54 , CYS B:111 , HIS B:153 , HIS B:157 , HOH B:199	BINDING SITE FOR RESIDUE ZN B 198

(no "SS Bond" information available for 1ZY0)

(no "Cis Peptide Bond" information available for 1ZY0)

(no "SAP(SNP)/Variant" information available for 1ZY0)

(no "PROSITE Motif" information available for 1ZY0)

(no "Exon" information available for 1ZY0)

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:191
 aligned with DEF1A_ARATH | Q9FV53 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:191
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268 
          DEF1A_ARATH    79 DLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPGVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCLSVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGPQ 269
               SCOP domains d1zy0a_ A: automated matches                                                                                                                                                                    SCOP domains
               CATH domains 1zy0A00 A:2-192 Peptide Deformylase                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh...........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeeehhhhhhh.hhhhhhhhh...eeeeeeeeeeeee....eeeeeeee..eeeeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhh...hhhhh......ee.hhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zy0 A   2 DLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPGVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCLSVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGSH 192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with DEF1A_ARATH | Q9FV53 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:191
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268 
          DEF1A_ARATH    79 DLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPGVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCLSVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGPQ 269
               SCOP domains d1zy0b_ B: automated matches                                                                                                                                                                    SCOP domains
               CATH domains 1zy0B00 B:2-192 Peptide Deformylase                                                                                                                                                             CATH domains
           Pfam domains (1) -Pep_deformylase-1zy0B01 B:3-173                                                                                                                                            ------------------- Pfam domains (1)
           Pfam domains (2) -Pep_deformylase-1zy0B02 B:3-173                                                                                                                                            ------------------- Pfam domains (2)
         Sec.struct. author .........hhhhhh...........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeee........hhhhhhhhh...eeeeeeeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhh...hhhhh......ee.hhhhh.........ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zy0 B   2 DLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPGVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCLSVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGSH 192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Peptide deformylase (87)

Superfamily: Peptide deformylase (87)

Family: automated matches (25)

Protein domain: automated matches (25)

Thale cress (Arabidopsis thaliana) [TaxId: 3702] (5)

1a	d1zy0a_	A:
1b	d1zy0b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Peptide Deformylase (68)

Homologous Superfamily: Peptide Deformylase (68)

Thale cress (Arabidopsis thaliana) (3)

1a	1zy0A00	A:2-192
1b	1zy0B00	B:2-192

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Pep_deformylase] (48)

Family: Pep_deformylase (48)

Arabidopsis thaliana (Mouse-ear cress) (13)

1a	Pep_deformylase-1zy0B01	B:3-173
1b	Pep_deformylase-1zy0B02	B:3-173

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DEF1A_ARATH | Q9FV53)

molecular function
	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:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0042586	peptide deformylase activity	Catalysis of the reaction: formyl-L-methionyl peptide + H2O = formate + methionyl peptide.
biological process
	GO:0043686	co-translational protein modification	The process of covalently altering one or more amino acids in a protein after translation has begun but before the protein has been released from the ribosome.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009570	chloroplast stroma	The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0009505	plant-type cell wall	A more or less rigid stucture lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

Asymmetric/Biological Unit
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	1zy0
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	DEF1A_ARATH \| Q9FV53	:	1zxz 1zy1 4je6 4je7 4je8

Description

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Ligands, Modified Residues, Ions (1, 2)

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