3G5P - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE AND ACTIVITY OF HUMAN MITOCHONDRIAL PEPTIDE DEFORMYLASE, A NOVEL CANCER TARGET

Authors :   S. Escobar-Alvarez, Y. Goldgur, G. Yang, O. Ouerfelli, Y. Li, D. A. Sche

Date :   05 Feb 09 (Deposition) - 07 Apr 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Peptide Deformylase, Human, Mitochondria, Hydrolase, Iron, Metal- Binding, Mitochondrion, Protein Biosynthesis, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Escobar-Alvarez, Y. Goldgur, G. Yang, O. Ouerfelli, Y. Li, D. A. Scheinberg
Structure And Activity Of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target
J. Mol. Biol. V. 387 1211 2009
PubMed-ID: 19236878 | Reference-DOI: 10.1016/J.JMB.2009.02.032

Molecule 1 - PEPTIDE DEFORMYLASE, MITOCHONDRIAL
	Chains	:	A, B, C, D
	EC Number	:	3.5.1.88
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PDF, PDF1A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	POLYPEPTIDE DEFORMYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	CO	4	Ligand/Ion	COBALT (II) ION
2	PO4	8	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN C:57 , CYS C:114 , HIS C:156 , HIS C:160 , PO4 C:187	BINDING SITE FOR RESIDUE CO C 1
02	AC2	SOFTWARE	GLN D:57 , CYS D:114 , HIS D:156 , HIS D:160 , PO4 D:187	BINDING SITE FOR RESIDUE CO D 2
03	AC3	SOFTWARE	PO4 A:2 , GLN A:57 , CYS A:114 , HIS A:156 , HIS A:160	BINDING SITE FOR RESIDUE CO A 186
04	AC4	SOFTWARE	GLN B:57 , CYS B:114 , HIS B:156 , HIS B:160 , PO4 B:188	BINDING SITE FOR RESIDUE CO B 186
05	AC5	SOFTWARE	PO4 A:2 , CYS A:50 , VAL A:51 , GLY A:52 , ILE A:153 , HOH A:323 , HOH A:342 , HOH A:359 , HOH A:391	BINDING SITE FOR RESIDUE PO4 A 1
06	AC6	SOFTWARE	PO4 A:1 , GLY A:52 , LEU A:53 , GLN A:57 , CYS A:114 , GLU A:115 , HIS A:156 , GLU A:157 , HIS A:160 , CO A:186 , HOH A:342	BINDING SITE FOR RESIDUE PO4 A 2
07	AC7	SOFTWARE	CYS B:50 , VAL B:51 , GLY B:52 , ILE B:153 , PO4 B:188 , HOH B:317 , HOH B:319 , HOH B:347	BINDING SITE FOR RESIDUE PO4 B 187
08	AC8	SOFTWARE	GLY B:52 , LEU B:53 , GLN B:57 , CYS B:114 , GLU B:115 , HIS B:156 , GLU B:157 , HIS B:160 , CO B:186 , PO4 B:187 , HOH B:317	BINDING SITE FOR RESIDUE PO4 B 188
09	AC9	SOFTWARE	CYS C:50 , VAL C:51 , GLY C:52 , PO4 C:187 , HOH C:302 , HOH C:328 , HOH C:335	BINDING SITE FOR RESIDUE PO4 C 186
10	BC1	SOFTWARE	CO C:1 , GLY C:52 , LEU C:53 , GLN C:57 , CYS C:114 , GLU C:115 , HIS C:156 , GLU C:157 , HIS C:160 , PO4 C:186 , HOH C:328	BINDING SITE FOR RESIDUE PO4 C 187
11	BC2	SOFTWARE	CYS D:50 , VAL D:51 , GLY D:52 , PO4 D:187 , HOH D:275 , HOH D:321 , HOH D:322	BINDING SITE FOR RESIDUE PO4 D 186
12	BC3	SOFTWARE	CO D:2 , GLY D:52 , LEU D:53 , GLN D:57 , CYS D:114 , GLU D:115 , HIS D:156 , GLU D:157 , HIS D:160 , PO4 D:186 , HOH D:321	BINDING SITE FOR RESIDUE PO4 D 187

(no "SS Bond" information available for 3G5P)

(no "Cis Peptide Bond" information available for 3G5P)

(no "SAP(SNP)/Variant" information available for 3G5P)

(no "PROSITE Motif" information available for 3G5P)

(no "Exon" information available for 3G5P)

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:183
 aligned with DEFM_HUMAN | Q9HBH1 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:193
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           DEFM_HUMAN    51 HLRRLVLGPPEPPFSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 243
               SCOP domains d3g          5pa_ A: automated matches                                                                                                                                                            SCOP domains
               CATH domains 3g5          pA00 A:3-185 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...----------........hhhhh......hhhhh.hhhhhhhhhhhhhhhhhhh..eee.hhhh....eeeeeehhhhhhh.hhhhhhhh....eeeeeeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhh.hhhhhee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5p A   3 HMS----------FSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 185
                              |      -   |    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   
                              5          6

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with DEFM_HUMAN | Q9HBH1 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:193
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           DEFM_HUMAN    51 HLRRLVLGPPEPPFSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 243
               SCOP domains d3g          5pb_ B: automated matches                                                                                                                                                            SCOP domains
               CATH domains 3g5          pB00 B:3-185 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...----------........hhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhh..eee.hhhh....eeeeeehhhhhhh.hhhhhhhh....eeeeeeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhh.hhhhhee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5p B   3 HMS----------FSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 185
                              |      -   |    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   
                              5          6

Chain C from PDB  Type:PROTEIN  Length:183
 aligned with DEFM_HUMAN | Q9HBH1 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:193
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           DEFM_HUMAN    51 HLRRLVLGPPEPPFSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 243
               SCOP domains d3g          5pc_ C: automated matches                                                                                                                                                            SCOP domains
               CATH domains 3g5          pC00 C:3-185 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...----------........hhhhh......hhhhh.hhhhhhhhhhhhhhhhhhh..eee.hhhh....eeeeeehhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhh.hhhhhee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5p C   3 HMS----------FSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 185
                              |      -   |    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   
                              5          6

Chain D from PDB  Type:PROTEIN  Length:183
 aligned with DEFM_HUMAN | Q9HBH1 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:193
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           DEFM_HUMAN    51 HLRRLVLGPPEPPFSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 243
               SCOP domains d3g          5pd_ D: automated matches                                                                                                                                                            SCOP domains
               CATH domains 3g5          pD00 D:3-185 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...----------........hhhhh......hhhhh.hhhhhhhhhhhhhhhhhhh..eee.hhhh....eeeeeehhhhhhhhhhhhhhhh....eeeeeeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhh.hhhhhee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5p D   3 HMS----------FSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 185
                              |      -   |    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   
                              5          6

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) (23004)

Fold: Peptide deformylase (87)

Superfamily: Peptide deformylase (87)

Family: automated matches (25)

Protein domain: automated matches (25)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d3g5pa_	A:
1b	d3g5pb_	B:
1c	d3g5pc_	C:
1d	d3g5pd_	D:

Asymmetric 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)

Human (Homo sapiens) (2)

1a	3g5pA00	A:3-185
1b	3g5pB00	B:3-185
1c	3g5pC00	C:3-185
1d	3g5pD00	D:3-185

(no "Pfam Domain" information available for 3G5P)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DEFM_HUMAN | Q9HBH1)

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:0031365	N-terminal protein amino acid modification	The alteration of the N-terminal amino acid residue in a protein.
	GO:0018206	peptidyl-methionine modification	The modification of peptidyl-methionine.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	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: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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3g5p)

Biological Units
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	3g5p
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	3.5.1.88
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	DEFM_HUMAN \| Q9HBH1	:	3g5k

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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