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(-) Description

Title :  CRYSTAL STRUCTURE OF METHIONINE AMINOPEPTIDASE 1B FROM PLASMODIUM FALCIPARUM, PF10_0150
 
Authors :  A. K. Wernimont, J. D. Artz, L. Crombet, J. Lew, J. Weadge, W. Tempel, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, R. Hui, T. Hill Structural Genomics Consortium (Sgc)
Date :  25 May 11  (Deposition) - 29 Jun 11  (Release) - 29 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Malaria, Proteolysis, "Pita Bread" Fold, Peptidase, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, J. D. Artz, L. Crombet, J. Lew, J. Weadge, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, R. Hui, T. Hill
Crystal Structure Of Methionine Aminopeptidase 1B From Plasmodium Falciparum, Pf10_0150
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHIONINE AMINOPEPTIDASE
    Chains: A
    EC Number: 3.4.11.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28MLH
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PF10_0150
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:230 , TYR A:255 , LYS A:362 , HOH A:450 , HOH A:527BINDING SITE FOR RESIDUE GOL A 369
2AC2SOFTWAREASP A:204 , HIS A:270 , GLU A:303 , GLU A:334 , HOH A:385 , HOH A:518BINDING SITE FOR RESIDUE FE A 370
3AC3SOFTWARELYS A:121 , ASP A:124 , TYR A:125 , THR A:351 , ASP A:353 , HOH A:530BINDING SITE FOR RESIDUE GOL A 371

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S6B)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:279 -Pro A:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S6B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S6B)

(-) Exons   (0, 0)

(no "Exon" information available for 3S6B)

(-) 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:345
 aligned with Q8IJP2_PLAF7 | Q8IJP2 from UniProtKB/TrEMBL  Length:517

    Alignment length:345
                                   181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511     
         Q8IJP2_PLAF7   172 HLKTIVKKHLSPENFDPTNRKYWVYDDHLKNFVNFKFTGDVRPWPLSKINHVPSHIERPDYAISSIPESELIYKRKSDIYVNNEEEIQRIREACILGRKTLDYAHTLVSPGVTTDEIDRKVHEFIIKNNAYPSTLNYYKFPKSCCTSVNEIVCHGIPDYRPLKSGDIINIDISVFYKGVHSDLNETYFVGDINDVPKEGKELVETCYFSLMEAIKKCKPGMFYKNIGTLIDAYVSKKNFSVVRSYSGHGVGKLFHSNPTVPHFKKNKAVGIMKPGHVFTIEPMINQGHYSDVLWPDQWTSATSDGKLSAQFEHTLLITNNGVEILTKRTQDSPPLGFDTKDELYY 516
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------Peptidase_M24-3s6bA01 A:110-341                                                                                                                                                                                                         -------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.........hhhhhhh.hhhhhh.................................hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..ee...hhhhh....eeee..eee.............eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...ee.....eee......eeeee................eeee..eee.....eee......eee.....eee..eeeeee..eeee...............hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s6b A  23 HLKTIVKKHLSPENFDPTNRKYWVYDDHLKNFVNFKFTGDVRPWPLSKINHVPSHIERPDYAISSIPESELIYKRKSDIYVNNEEEIQRIREACILGRKTLDYAHTLVSPGVTTDEIDRKVHEFIIKNNAYPSTLNYYKFPKSCCTSVNEIVCHGIPDYRPLKSGDIINIDISVFYKGVHSDLNETYFVGDINDVPKEGKELVETCYFSLMEAIKKCKPGMFYKNIGTLIDAYVSKKNFSVVRSYSGHGVGKLFHSNPTVPHFKKNKAVGIMKPGHVFTIEPMINQGHYSDVLWPDQWTSATSDGKLSAQFEHTLLITNNGVEILTKRTQDSPPLGFDTKDELYY 367
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 3S6B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S6B)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Peptidase_M24] (23)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8IJP2_PLAF7 | Q8IJP2)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0070006    metalloaminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008235    metalloexopeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
biological process
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0070084    protein initiator methionine removal    The protein modification process in which the translation-initiating methionine or formylmethionine residue is removed from a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0022626    cytosolic ribosome    A ribosome located in the cytosol.

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