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(-) Description

Title :  STRUCTURAL AND KINETIC BASES FOR THE METAL PREFERENCE OF THE M18 AMINOPEPTIDASE FROM PSEUDOMONAS AERUGINOSA
 
Authors :  D. D. Nguyen, R. Pandian, D. D. Kim, S. C. Ha, H. J. Yoon, K. S. Kim, K. H. Yun K. K. Kim
Date :  19 Jan 14  (Deposition) - 02 Apr 14  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (3x),B (3x),C (3x),D (3x)
Keywords :  Dodecameric Tet Structure, Aspartyl Aminopeptidase, Pseudomonas Aeruginosa, Aspartic Mutation, M18 Family, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. D. Nguyen, R. Pandian, D. Kim, S. C. Ha, H. J. Yoon, K. S. Kim, K. H. Yun, J. H. Kim, K. K. Kim
Structural And Kinetic Bases For The Metal Preference Of Th M18 Aminopeptidase From Pseudomonas Aeruginosa
Biochem. Biophys. Res. Commun. V. 447 101 2014
PubMed-ID: 24704201  |  Reference-DOI: 10.1016/J.BBRC.2014.03.109

(-) Compounds

Molecule 1 - PROBABLE M18 FAMILY AMINOPEPTIDASE 2
    Chains: A, B, C, D
    EC Number: 3.4.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: APEB, PA 3247, PA3247
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA PAO1
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): A (3x)B (3x)C (3x)D (3x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4OID)

(-) Sites  (0, 0)

(no "Site" information available for 4OID)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OID)

(-) Cis Peptide Bonds  (17, 17)

Asymmetric Unit
No.Residues
1Ala A:181 -Pro A:182
2Pro A:182 -Gly A:183
3Ala A:236 -Asn A:237
4Ser A:426 -Glu A:427
5Arg B:2 -Ala B:3
6Trp B:44 -His B:45
7Pro B:182 -Gly B:183
8Ala B:236 -Asn B:237
9Ser B:338 -Asn B:339
10Arg C:2 -Ala C:3
11Pro C:182 -Gly C:183
12Gly C:183 -Glu C:184
13Ala C:236 -Asn C:237
14Met C:400 -His C:401
15Arg D:2 -Ala D:3
16Ala D:236 -Asn D:237
17Met D:400 -His D:401

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OID)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OID)

(-) Exons   (0, 0)

(no "Exon" information available for 4OID)

(-) 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:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee.............eeeeee...eeeeee....hhhhhheeeeeee....eeeeeeeeeeee..eeeeeeeee....hhhhh...eeeeeeeeeee..eeeeeeee...........hhhhh.hhhhh...hhhhhh..eeee.......hhhhhhhhhhhhhhh....eeeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhh....eeeeeee......hhhhhhhh.....hhhhhhhh..eeeeeeeee.....hhhhh............eeee........hhhhhhhhhhhhhhh....eeee..........eeeeeeeee......eeee.hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oid A   1 MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTETGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVGAHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRAANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLANLLSCHAGLEALLNAEGDENCILVCTDHEEVPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADRHDANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMQVGVRTVDIGLPTFAMHSIRELAGSHDLAHLVKVLGAFYASSELP 429
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      |280       290       300       310       320       330       340       350       360       370 ||    392       402       412       422       
                                                                                                                                                                                                                                                                                                    267|                                                                                           372|                                            
                                                                                                                                                                                                                                                                                                     278                                                                                            385                                            


Chain B from PDB  Type:PROTEIN  Length:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee.............eeeeee...eeeeee....hhhhhheeeeeee....eeeeeeeeeeee..eeeeeeeee....hhhhh...eeeeeeeeeee..eeeeeeee...........hhhhh.hhhhh...hhhhhh..eeee.......hhhhhhhhhhhhhhh....eeeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhh....eeeeeee......hhhhhhhhh....hhhhhhhhh.eeeee..ee.....hhhhh............eeee........hhhhhhhhhhhhhhh....eeee..........eeeee.eee......eeee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oid B   1 MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTETGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVGAHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRAANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLANLLSCHAGLEALLNAEGDENCILVCTDHEEVPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADRHDANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMQVGVRTVDIGLPTFAMHSIRELAGSHDLAHLVKVLGAFYASSELP 429
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      |280       290       300       310       320       330       340       350       360       370 ||    392       402       412       422       
                                                                                                                                                                                                                                                                                                    267|                                                                                           372|                                            
                                                                                                                                                                                                                                                                                                     278                                                                                            385                                            


Chain C from PDB  Type:PROTEIN  Length:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee..............eeeee...eeeeee....hhhhhh.eeeeee....eeeeeeeeeeee..eeeeeeeee....hhhhh...eeeeeeeeeee..eeeeeeee...........hhhhh.hhhhh...hhhhhh..eeee.......hhhhhhhhhhhhhhh....eeeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhh.....eeeeee......hhhhhhhhh....hhhhhhhh..eeeee..ee.....hhhhh............eeee........hhhhhhhhhhhhhhh....eeee..........eeeee.eee......eeee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oid C   1 MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTETGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVGAHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRAANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLANLLSCHAGLEALLNAEGDENCILVCTDHEEVPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADRHDANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMQVGVRTVDIGLPTFAMHSIRELAGSHDLAHLVKVLGAFYASSELP 429
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      |280       290       300       310       320       330       340       350       360       370 ||    392       402       412       422       
                                                                                                                                                                                                                                                                                                    267|                                                                                           372|                                            
                                                                                                                                                                                                                                                                                                     278                                                                                            385                                            


Chain D from PDB  Type:PROTEIN  Length:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee.............eeeeee...eeeeee....hhhhhheeeeeee....eeeeeeeeeeee..eeeeeeeee....hhhhh...eeeeeeeeeee..eeeeeeee...........hhhhhhhhhhh...hhhhhh..eeee.......hhhhhhhhhhhhhhh....eeeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhh....eeeeeee......hhhhhhhh.....hhhhhhhhh.eeeeeeeee.....hhhhh............eee.........hhhhhhhhhhhhhhhh...eee...........eeeeeeeee......eeee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oid D   1 MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTETGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVGAHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRAANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLANLLSCHAGLEALLNAEGDENCILVCTDHEEVPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADRHDANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMQVGVRTVDIGLPTFAMHSIRELAGSHDLAHLVKVLGAFYASSELP 429
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      |280       290       300       310       320       330       340       350       360       370 ||    392       402       412       422       
                                                                                                                                                                                                                                                                                                    267|                                                                                           372|                                            
                                                                                                                                                                                                                                                                                                     278                                                                                            385
   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  (0, 0)

(no "SCOP Domain" information available for 4OID)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OID)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OID)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:181 - Pro A:182   [ RasMol ]  
    Ala A:236 - Asn A:237   [ RasMol ]  
    Ala B:236 - Asn B:237   [ RasMol ]  
    Ala C:236 - Asn C:237   [ RasMol ]  
    Ala D:236 - Asn D:237   [ RasMol ]  
    Arg B:2 - Ala B:3   [ RasMol ]  
    Arg C:2 - Ala C:3   [ RasMol ]  
    Arg D:2 - Ala D:3   [ RasMol ]  
    Gly C:183 - Glu C:184   [ RasMol ]  
    Met C:400 - His C:401   [ RasMol ]  
    Met D:400 - His D:401   [ RasMol ]  
    Pro A:182 - Gly A:183   [ RasMol ]  
    Pro B:182 - Gly B:183   [ RasMol ]  
    Pro C:182 - Gly C:183   [ RasMol ]  
    Ser A:426 - Glu A:427   [ RasMol ]  
    Ser B:338 - Asn B:339   [ RasMol ]  
    Trp B:44 - His B:45   [ RasMol ]  
 
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 Related Entries

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

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        APEB_PSEAE | Q9HYZ3: 2ijz 3wt4 4njq 4njr 4oiw

(-) Related Entries Specified in the PDB File

4njq COCOPAAP ASPARTYL AMINO PEPTIDASE OF PSEUDOMONAS AERUGINOSA WITH ZINC IN CATALYTIC SITE
4njr [ZNZN-PAAP], ASPARTYL AMINO PEPTIDASE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH ZINC
4oiw