1G2A - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WITH ACTINONIN

Authors :   J. M. Clements, P. Beckett, A. Brown, C. Catlin, M. Lobell, S. Palan, W. Thomas, M. Whittaker, P. J. Baker, H. F. Rodgers, V. Barynin, D. W. Rice, M. G. Hunter

Date :   18 Oct 00 (Deposition) - 17 Oct 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Actinonin, Inhibition, Polypeptide Deformylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Clements, R. P. Beckett, A. Brown, G. Catlin, M. Lobell, S. Palan, W. Thomas, M. Whittaker, S. Wood, S. Salama, P. J. Baker, H. F. Rodgers, V. Barynin, D. W. Rice, M. G. Hunter
Antibiotic Activity And Characterization Of Bb-3497, A Novel Peptide Deformylase Inhibitor.
Antimicrob. Agents Chemother. V. 45 563 2001
PubMed-ID: 11158755 | Reference-DOI: 10.1128/AAC.45.2.563-570.2001
(for further references see the PDB file header)

Molecule 1 - POLYPEPTIDE DEFORMYLASE
	Chains	:	A, B, C
	EC Number	:	3.5.1.31
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET24-PDF
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DEF
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	N-FORMYLMETHIONYLAMINOACYL-TRNA DEFORMYLASE, PDF, FMS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	BB2	3	Ligand/Ion	ACTINONIN
2	NI	3	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BB2	1	Ligand/Ion	ACTINONIN
2	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BB2	1	Ligand/Ion	ACTINONIN
2	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	BB2	1	Ligand/Ion	ACTINONIN
2	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:50 , CYS A:90 , HIS A:132 , HIS A:136 , BB2 A:1001	BINDING SITE FOR RESIDUE NI A 1169
2	AC2	SOFTWARE	GLN B:50 , CYS B:90 , HIS B:132 , HIS B:136 , BB2 B:2002	BINDING SITE FOR RESIDUE NI B 2169
3	AC3	SOFTWARE	GLN C:50 , CYS C:90 , HIS C:132 , HIS C:136 , BB2 C:3003	BINDING SITE FOR RESIDUE NI C 3169
4	AC4	SOFTWARE	GLU A:42 , GLY A:43 , ILE A:44 , GLY A:45 , GLN A:50 , GLU A:87 , GLY A:89 , CYS A:90 , LEU A:91 , ARG A:97 , HIS A:132 , GLU A:133 , HIS A:136 , NI A:1169	BINDING SITE FOR RESIDUE BB2 A 1001
5	AC5	SOFTWARE	GLU B:42 , GLY B:43 , ILE B:44 , GLY B:45 , GLN B:50 , GLU B:87 , GLU B:88 , GLY B:89 , CYS B:90 , LEU B:91 , ARG B:97 , HIS B:132 , GLU B:133 , HIS B:136 , NI B:2169	BINDING SITE FOR RESIDUE BB2 B 2002
6	AC6	SOFTWARE	GLY C:43 , ILE C:44 , GLY C:45 , GLN C:50 , GLU C:87 , GLY C:89 , CYS C:90 , LEU C:91 , ARG C:97 , HIS C:132 , GLU C:133 , HIS C:136 , NI C:3169 , HOH C:3184 , HOH C:3226	BINDING SITE FOR RESIDUE BB2 C 3003

(no "SS Bond" information available for 1G2A)

Asymmetric Unit

No.	Residues
1	Ile A:8	-	Pro A:9
2	Ile B:8	-	Pro B:9
3	Ile C:8	-	Pro C:9

(no "SAP(SNP)/Variant" information available for 1G2A)

(no "PROSITE Motif" information available for 1G2A)

(no "Exon" information available for 1G2A)

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
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Chain A from PDB  Type:PROTEIN  Length:164
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            DEF_ECOLI     2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 165
               SCOP domains d1g2aa_ A: Peptide deformylase                                                                                                                                       SCOP domains
               CATH domains 1g2aA00 A:1-164 Peptide Deformylase                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.........eeeeeeeeeeee.....eeee..eeeeeee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g2a A   1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            DEF_ECOLI     2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 165
               SCOP domains d1g2ab_ B: Peptide deformylase                                                                                                                                       SCOP domains
               CATH domains 1g2aB00 B:1-164 Peptide Deformylase                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.........eeeeeeeeeeee.....eeee..eeeeeee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g2a B   1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:164
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            DEF_ECOLI     2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 165
               SCOP domains d1g2ac_ C: Peptide deformylase                                                                                                                                       SCOP domains
               CATH domains 1g2aC00 C:1-164 Peptide Deformylase                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.........eeeeeeeeeeee.....eeee..eeeeeee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g2a C   1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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: Peptide deformylase (87)

Superfamily: Peptide deformylase (87)

Family: Peptide deformylase (62)

Protein domain: Peptide deformylase (50)

Escherichia coli [TaxId: 562] (21)

1a	d1g2aa_	A:
1b	d1g2ab_	B:
1c	d1g2ac_	C:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Peptide Deformylase (68)

Homologous Superfamily: Peptide Deformylase (68)

Escherichia coli. Organism_taxid: 562. (3)

1a	1g2aA00	A:1-164
1b	1g2aB00	B:1-164
1c	1g2aC00	C:1-164

(no "Pfam Domain" information available for 1G2A)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (DEF_ECOLI | P0A6K3)

molecular function
	GO:0008198	ferrous iron binding	Interacting selectively and non-covalently with ferrous iron, Fe(II).
	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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0031365	N-terminal protein amino acid modification	The alteration of the N-terminal amino acid residue in a protein.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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