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(-) Description

Title :  CRYSTAL STRUCTURE OF S. AUREUS PEPTIDE DEFORMYLASE
 
Authors :  E. T. Baldwin, M. S. Harris
Date :  01 May 02  (Deposition) - 12 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Zinc Peptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. T. Baldwin, M. S. Harris, A. W. Yem, C. L. Wolfe, A. F. Vosters, K. A. Curry, R. W. Murray, J. H. Bock, V. P. Marshall, J. I. Cialdella, M. H. Merchant, G. Choi, M. R. Deibel Jr.
Crystal Structure Of Type Ii Peptide Deformylase From Staphylococcus Aureus
J. Biol. Chem. V. 277 31163 2002
PubMed-ID: 12048187  |  Reference-DOI: 10.1074/JBC.M202750200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (S.AUREUS PEPTIDE DEFORMYLASE)
    Chains: A
    EC Number: 3.5.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE60
    Expression System Strain: JM109
    Expression System Taxid: 562
    Gene: DEF
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:65 , CYS A:111 , HIS A:154 , HIS A:158 , HOH A:186 , HOH A:281BINDING SITE FOR RESIDUE ZN A 185

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:24 -Pro A:25

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1LMH)

(-) Sequences/Alignments

Asymmetric/Biological 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:184
 aligned with DEF_STAAM | P68825 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:184
                                                                                                                                                                                                                183 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  | 
            DEF_STAAM     1 MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV-   -
               SCOP domains d1lmha_ A: Peptide deformylase                                                                                                                                                           SCOP domains
               CATH domains -1lmhA00 A:2-184 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains ---Pep_deformylase-1lmhA01 A:4-174                                                                                                                                            ---------- Pfam domains
         Sec.struct. author ..hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.hhhh....eeeeee........eeeeeeeeeeeee...eee...................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh............ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lmh A   1 mLTmKDIIRDGHPTLRQKAAELELPLTKEEKETLIAmREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRmIAVLIPDDGSGKSYDYmLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNKITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVmFYDHIDKDHPLQPHTDAVEVH 184
                            |  |    10        20        30      | 40        50        60        70 |      80        90       100       110       120       130       140       150       160  |    170       180    
                            |  |                               37-MSE                             72-MSE           89-MSE                                                                   163-MSE                 
                            1-MSE                                                                                                                                                                                   
                               4-MSE                                                                                                                                                                                


Chain A from PDB  Type:PROTEIN  Length:184
 aligned with DEF_STAAN | P99077 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:184
                                                                                                                                                                                                                183 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  | 
            DEF_STAAN     1 MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV-   -
               SCOP domains d1lmha_ A: Peptide deformylase                                                                                                                                                           SCOP domains
               CATH domains -1lmhA00 A:2-184 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains ---Pep_deformylase-1lmhA01 A:4-174                                                                                                                                            ---------- Pfam domains
         Sec.struct. author ..hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.hhhh....eeeeee........eeeeeeeeeeeee...eee...................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh............ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lmh A   1 mLTmKDIIRDGHPTLRQKAAELELPLTKEEKETLIAmREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRmIAVLIPDDGSGKSYDYmLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNKITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVmFYDHIDKDHPLQPHTDAVEVH 184
                            |  |    10        20        30      | 40        50        60        70 |      80        90       100       110       120       130       140       150       160  |    170       180    
                            1-MSE                              37-MSE                             72-MSE           89-MSE                                                                   163-MSE                 
                               4-MSE                                                                                                                                                                                


Chain A from PDB  Type:PROTEIN  Length:184
 aligned with DEF_STAAU | P68826 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:184
                                                                                                                                                                                                                183 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  | 
            DEF_STAAU     1 MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV-   -
               SCOP domains d1lmha_ A: Peptide deformylase                                                                                                                                                           SCOP domains
               CATH domains -1lmhA00 A:2-184 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains ---Pep_deformylase-1lmhA01 A:4-174                                                                                                                                            ---------- Pfam domains
         Sec.struct. author ..hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.hhhh....eeeeee........eeeeeeeeeeeee...eee...................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh............ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lmh A   1 mLTmKDIIRDGHPTLRQKAAELELPLTKEEKETLIAmREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRmIAVLIPDDGSGKSYDYmLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNKITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVmFYDHIDKDHPLQPHTDAVEVH 184
                            |  |    10        20        30      | 40        50        60        70 |      80        90       100       110       120       130       140       150       160  |    170       180    
                            1-MSE                              37-MSE                             72-MSE           89-MSE                                                                   163-MSE                 
                               4-MSE
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Pep_deformylase] (48)

(-) Gene Ontology  (5, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DEF_STAAN | P99077)
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.

Chain A   (DEF_STAAM | P68825)
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.

Chain A   (DEF_STAAU | P68826)
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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DEF_STAAU | P68826: 1lm4 1lqw 1q1y 2ai9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1LMH)