1LME - JenaLib

Title :   CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM THERMOTOGA MARITIMA

Authors :   A. Kreusch, G. Spraggon, C. C. Lee, H. Klock, D. Mcmullan, K. Ng, T. Shin, J. Vincent, I. Warner, C. Ericson, S. A. Lesley, Joint Center For Structural Genomics (Jcsg)

Date :   01 May 02 (Deposition) - 24 Jun 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Thermophile, Pdf, Peptide Deformylase, Metalloenzyme, Deformylation, Structural Genomics, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Jcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Kreusch, G. Spraggon, C. C. Lee, H. Klock, D. Mcmullan, K. Ng, T. Shin, J. Vincent, I. Warner, C. Ericson, S. A. Lesley
Structure Analysis Of Peptide Deformylases From Streptococcus Pneumoniae, Staphylococcus Aureus, Thermotoga Maritima, And Pseudomonas Aeruginosa: Snapshots Of The Oxygen Sensitivity Of Peptide Deformylase
J. Mol. Biol. V. 330 309 2003
PubMed-ID: 12823970 | Reference-DOI: 10.1016/S0022-2836(03)00596-5
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

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

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:154
 aligned with DEF_THEMA | P96113 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:154
                                     1                                                                                                                                                
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141    
            DEF_THEMA     - ---------MYRIRVFGDPVLRKRAKPVTKFDENLKKTIERMIETMYHYDGVGLAAPQVGISQRFFVMDVGNGPVAVINPEILEIDPETEVAEEGCLSFPEIFVEIERSKRIKVKYQNTRGEYVEEELEGYAARVFQHEFDHLNGVLIIDRISP 145
               SCOP domains d1lmea_ A: Peptide deformylase                                                                                                                             SCOP domains
               CATH domains 1lmeA00 A:-8-145 Peptide Deformylase                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhh.........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee......eeeeeeeeeee...eeeeee.........eeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lme A  -8 DKIHHHHHHMYRIRVFGDPVLRKRAKPVTKFDENLKKTIERMIETMYHYDGVGLAAPQVGISQRFFVMDVGNGPVAVINPEILEIDPETEVAEEGcLSFPEIFVEIERSKRIKVKYQNTRGEYVEEELEGYAARVFQHEFDHLNGVLIIDRISP 145
                                     1        11        21        31        41        51        61        71        81     |  91       101       111       121       131       141    
                                                                                                                          87-OCS

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with DEF_THEMA | P96113 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:147
                              1                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       
            DEF_THEMA     - --MYRIRVFGDPVLRKRAKPVTKFDENLKKTIERMIETMYHYDGVGLAAPQVGISQRFFVMDVGNGPVAVINPEILEIDPETEVAEEGCLSFPEIFVEIERSKRIKVKYQNTRGEYVEEELEGYAARVFQHEFDHLNGVLIIDRISP 145
               SCOP domains d1lmeb_ B: Peptide deformylase                                                                                                                      SCOP domains
               CATH domains 1lmeB00 B:-1-145 Peptide Deformylase                                                                                                                CATH domains
           Pfam domains (1) --Pep_deformylase-1lmeB01 B:1-145                                                                                                                   Pfam domains (1)
           Pfam domains (2) --Pep_deformylase-1lmeB02 B:1-145                                                                                                                   Pfam domains (2)
         Sec.struct. author ..........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee......eeeeeeeeeee...eeeeee.........eeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lme B  -1 HHMYRIRVFGDPVLRKRAKPVTKFDENLKKTIERMIETMYHYDGVGLAAPQVGISQRFFVMDVGNGPVAVINPEILEIDPETEVAEEGcLSFPEIFVEIERSKRIKVKYQNTRGEYVEEELEGYAARVFQHEFDHLNGVLIIDRISP 145
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       
                                                                                                                   87-OCS

Legend:		→ Mismatch	(orange background)
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		→ 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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DEF_THEMA | P96113)

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: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.

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