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Title :   CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM VRE-E.FAECIUM

Authors :   K. Y. Hwang, K. H. Nam

Date :   21 Mar 08 (Deposition) - 13 Jan 09 (Release) - 13 Jan 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Pdf, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. H. Nam, J. I. Ham, A. Priyadarshi, E. E. Kim, N. Chung, K. Y. Hwang
Insight Into The Antibacterial Drug Design And Architectural Mechanism Of Peptide Recognition From The E. Faecium Peptide Deformylase Structure.
Proteins V. 74 261 2009
PubMed-ID: 18831047 | Reference-DOI: 10.1002/PROT.22257
(for further references see the PDB file header)

Molecule 1 - PEPTIDE DEFORMYLASE
	Chains	:	A, B
	EC Number	:	3.5.1.88
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	STREPTOCOCCUS FAECIUM
	Organism Scientific	:	ENTEROCOCCUS FAECIUM
	Organism Taxid	:	1352

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 14)

No.	Name	Count	Type	Full Name
1	FE	2	Ligand/Ion	FE (III) ION
2	MLI	4	Ligand/Ion	MALONATE ION
3	NA	8	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	MLI	3	Ligand/Ion	MALONATE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	MLI	1	Ligand/Ion	MALONATE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:65 , CYS A:114 , HIS A:157 , HIS A:161	BINDING SITE FOR RESIDUE FE A 188
02	AC2	SOFTWARE	GLN B:65 , CYS B:114 , HIS B:157 , HIS B:161	BINDING SITE FOR RESIDUE FE B 188
03	AC3	SOFTWARE	GLY A:113 , HIS A:157	BINDING SITE FOR RESIDUE NA A 189
04	AC4	SOFTWARE	LYS B:148 , GLU B:151	BINDING SITE FOR RESIDUE NA B 190
05	AC5	SOFTWARE	GLY B:113	BINDING SITE FOR RESIDUE NA B 191
06	AC6	SOFTWARE	ASP A:5 , GLU B:181	BINDING SITE FOR RESIDUE NA B 192
07	AC7	SOFTWARE	GLU B:10 , TYR B:168	BINDING SITE FOR RESIDUE NA B 193
08	AC8	SOFTWARE	SER B:100 , HIS B:101 , ARG B:146	BINDING SITE FOR RESIDUE NA B 194
09	AC9	SOFTWARE	GLU A:36	BINDING SITE FOR RESIDUE NA A 190
10	BC1	SOFTWARE	GLY A:58 , GLY A:60 , GLN A:65 , GLY A:113 , CYS A:114 , LEU A:115 , HIS A:157 , GLU A:158 , HIS A:161	BINDING SITE FOR RESIDUE MLI A 191
11	BC2	SOFTWARE	GLY B:58 , GLY B:60 , GLN B:65 , GLY B:113 , CYS B:114 , LEU B:115 , GLU B:158	BINDING SITE FOR RESIDUE MLI B 195
12	BC3	SOFTWARE	SER A:23 , ASP A:30 , LYS A:70 , LYS B:130 , ARG B:146	BINDING SITE FOR RESIDUE MLI A 192
13	BC4	SOFTWARE	GLU A:10 , ARG A:16 , TYR A:168	BINDING SITE FOR RESIDUE MLI A 193

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

Asymmetric Unit

No.	Residues
1	Leu A:24	-	Pro A:25
2	Leu B:24	-	Pro B:25

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

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

(no "Exon" information available for 3CMD)

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:186
 aligned with Q842S4_ENTFC | Q842S4 from UniProtKB/TrEMBL  Length:187

    Alignment length:194
                                   1                                                                                                                                                                                          
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183    
         Q842S4_ENTFC     - -------MITMDDIIREGNPTLREVAKEVSLPLSEEDISLGKEMLEFLKNSQDPIKAEELHLRGGVGLAAPQLDISKRIIAVHVPSPDPEADGPSLSTVMYNPKILSHSVQDACLGEGEGCLSVDREVPGYVVRHAKITVSYYDMNGEKHKIRLKNYESIVVQHEIDHINGVMFYDHINDQNPFALKEGVLVIE 187
               SCOP domains d3cmda_ A: automated matches                                                                                                                                                                       SCOP domains
               CATH domains 3cmdA00 A:-6-187 Peptide Deformylase                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.hhhh....eeeeee..--------.eeeeeeeeeeeee...eeee..................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhh...hhhhhh............eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cmd A  -6 LVPGRHMMITMDDIIREGNPTLREVAKEVSLPLSEEDISLGKEMLEFLKNSQDPIKAEELHLRGGVGLAAPQLDISKRIIAVHVPS--------SLSTVMYNPKILSHSVQDACLGEGEGCLSVDREVPGYVVRHAKITVSYYDMNGEKHKIRLKNYESIVVQHEIDHINGVMFYDHINDQNPFALKEGVLVIE 187
                                     3        13        23        33        43        53        63        73     |   -    |   93       103       113       123       133       143       153       163       173       183    
                                                                                                                79       88

Chain B from PDB  Type:PROTEIN  Length:188
 aligned with Q842S4_ENTFC | Q842S4 from UniProtKB/TrEMBL  Length:187

    Alignment length:196
                                     1                                                                                                                                                                                          
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      
         Q842S4_ENTFC     - ---------MITMDDIIREGNPTLREVAKEVSLPLSEEDISLGKEMLEFLKNSQDPIKAEELHLRGGVGLAAPQLDISKRIIAVHVPSPDPEADGPSLSTVMYNPKILSHSVQDACLGEGEGCLSVDREVPGYVVRHAKITVSYYDMNGEKHKIRLKNYESIVVQHEIDHINGVMFYDHINDQNPFALKEGVLVIE 187
               SCOP domains d3cmdb_ B: automated matches                                                                                                                                                                         SCOP domains
               CATH domains 3cmdB00 B:-8-187 Peptide Deformylase                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee...hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.hhhh....eeeeee..--------.eeeeeeeeeeeee...eeee..................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhh...hhhhhh............eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cmd B  -8 SGLVPGRHMMITMDDIIREGNPTLREVAKEVSLPLSEEDISLGKEMLEFLKNSQDPIKAEELHLRGGVGLAAPQLDISKRIIAVHVPS--------SLSTVMYNPKILSHSVQDACLGEGEGCLSVDREVPGYVVRHAKITVSYYDMNGEKHKIRLKNYESIVVQHEIDHINGVMFYDHINDQNPFALKEGVLVIE 187
                                     1        11        21        31        41        51        61        71       | -      | 91       101       111       121       131       141       151       161       171       181      
                                                                                                                  79       88

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: Peptide deformylase (62)

Protein domain: automated matches (12)

Enterococcus faecium [TaxId: 1352] (1)

1a	d3cmda_	A:
1b	d3cmdb_	B:

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)

Streptococcus faecium (Enterococcus faecium) (1)

1a	3cmdA00	A:-6-187
1b	3cmdB00	B:-8-187

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q842S4_ENTFC | Q842S4)

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: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.

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Description

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Ligands, Modified Residues, Ions (3, 14)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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