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(-) Description

Title :  STRUCTURE OF PEPTIDE DEFORMYLASE FROM STAPHYLOCOCCUS AUREUS AT 1.45 A
 
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
Date :  30 Apr 02  (Deposition) - 24 Jun 03  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pdf, Metalloenzyme, Staphylococcus Aureus, 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

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE PDF1
    Chains: A, B
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMH1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PDF1
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2GOL1Ligand/IonGLYCEROL
3OCS2Mod. Amino AcidCYSTEINESULFONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GOL-1Ligand/IonGLYCEROL
3OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GOL1Ligand/IonGLYCEROL
3OCS1Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:-10 , OCS A:111 , HIS A:154 , HIS A:158BINDING SITE FOR RESIDUE FE A 603
2AC2SOFTWAREGLN B:65 , OCS B:111 , HIS B:154 , HIS B:158 , HOH B:616BINDING SITE FOR RESIDUE FE B 603
3AC3SOFTWAREGLU B:109 , GLY B:110 , TYR B:147 , HIS B:154 , HOH B:687 , HOH B:784 , HOH B:866BINDING SITE FOR RESIDUE GOL B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LM4)

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LM4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LM4)

(-) Exons   (0, 0)

(no "Exon" information available for 1LM4)

(-) 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:190
 aligned with DEF_STAAU | P68826 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:190
                                   1                                                                                                                                                                                      
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183
            DEF_STAAU     - -------MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV 183
               SCOP domains d1lm4a_ A: Peptide deformylase                                                                                                                                                                 SCOP domains
               CATH domains 1lm4A00 A:-10-183 Peptide Deformylase                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh....eeeeee........eeeeeeeeeeeee...eee...................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh............ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lm4 A -10 GSDKIHHMLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGcLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV 183
                                 ||  3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183
                                -5|                                                                                                            111-OCS                                                                    
                                  0                                                                                                                                                                                       


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

    Alignment length:184
                             1                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    
            DEF_STAAU     - -MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV 183
               SCOP domains d1lm4b_ B: Peptide deformylase                                                                                                                                                           SCOP domains
               CATH domains 1lm4B00 B:0-183 Peptide Deformylase                                                                                                                                                      CATH domains
           Pfam domains (1) ----Pep_deformylase-1lm4B01 B:4-174                                                                                                                                            --------- Pfam domains (1)
           Pfam domains (2) ----Pep_deformylase-1lm4B02 B:4-174                                                                                                                                            --------- Pfam domains (2)
         Sec.struct. author ...hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh....eeeeee........eeeeeeeeeeeee...eee...................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh............ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lm4 B   0 HMLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGcLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV 183
                                     9        19        29        39        49        59        69        79        89        99       109 |     119       129       139       149       159       169       179    
                                                                                                                                         111-OCS
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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: 1lmh 1lqw 1q1y 2ai9

(-) Related Entries Specified in the PDB File

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