1XEM - JenaLib

Title :   HIGH RESOLUTION CRYSTAL STRUCTURE OF ESCHERICHIA COLI ZINC- PEPTIDE DEFORMYLASE BOUND TO FORMATE

Authors :   R. Jain, B. Hao, R. -P. Liu, M. K. Chan

Date :   10 Sep 04 (Deposition) - 29 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.76

Chains :   Asym./Biol. Unit : A

Keywords :   Zinc Deformylase, Formate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Jain, B. Hao, R. -P. Liu, M. K. Chan
Structures Of E. Coli Peptide Deformylase Bound To Formate: Insight Into The Preference For Fe2+ Over Zn2+ As The Activ Site Metal
J. Am. Chem. Soc. V. 127 4558 2005
PubMed-ID: 15796505 | Reference-DOI: 10.1021/JA0503074

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 11)

Sites (11, 11)

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:50 , CYS A:90 , HIS A:132 , HIS A:136 , FMT A:501	BINDING SITE FOR RESIDUE ZN A 401
02	AC2	SOFTWARE	GLY A:45 , GLN A:50 , CYS A:90 , LEU A:91 , HIS A:132 , GLU A:133 , HIS A:136 , ZN A:401	BINDING SITE FOR RESIDUE FMT A 501
03	AC3	SOFTWARE	ARG A:69 , VAL A:71 , ARG A:113 , FMT A:505 , HOH A:519 , HOH A:562 , HOH A:572 , HOH A:630 , HOH A:644	BINDING SITE FOR RESIDUE FMT A 502
04	AC4	SOFTWARE	GLN A:131 , MET A:134 , FMT A:509 , HOH A:546 , HOH A:590 , HOH A:596 , HOH A:736	BINDING SITE FOR RESIDUE FMT A 503
05	AC5	SOFTWARE	ILE A:8 , PRO A:9 , ASP A:10 , ARG A:14 , HOH A:671 , HOH A:674 , HOH A:718	BINDING SITE FOR RESIDUE FMT A 504
06	AC6	SOFTWARE	ASP A:112 , ASP A:114 , FMT A:502 , HOH A:562 , HOH A:630 , HOH A:683	BINDING SITE FOR RESIDUE FMT A 505
07	AC7	SOFTWARE	LYS A:80 , SER A:81 , HOH A:580 , HOH A:637 , HOH A:707	BINDING SITE FOR RESIDUE FMT A 506
08	AC8	SOFTWARE	LYS A:80 , GLU A:83 , FMT A:509 , HOH A:574 , HOH A:594 , HOH A:596 , HOH A:669 , HOH A:726 , HOH A:736	BINDING SITE FOR RESIDUE FMT A 507
09	AC9	SOFTWARE	HIS A:7 , GLU A:41 , HOH A:575 , HOH A:748 , HOH A:786	BINDING SITE FOR RESIDUE FMT A 508
10	BC1	SOFTWARE	GLN A:131 , ASP A:135 , TYR A:145 , FMT A:503 , FMT A:507 , HOH A:521 , HOH A:574 , HOH A:669	BINDING SITE FOR RESIDUE FMT A 509
11	BC2	SOFTWARE	GLU A:95 , GLN A:96 , LYS A:157 , HOH A:545 , HOH A:577 , HOH A:716 , HOH A:734	BINDING SITE FOR RESIDUE FMT A 510

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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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 d1xema_ A: Peptide deformylase                                                                                                                                       SCOP domains
               CATH domains 1xemA00 A:1-164 Peptide Deformylase                                                                                                                                  CATH domains
               Pfam domains -Pep_deformylase-1xemA01 A:2-152                                                                                                                        ------------ Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.........eeeeeeeeeeee.....ee.........ee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xem A   1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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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