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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. Y. Kim, S. C. Ha, K. H. Yun, K. S. Kim, J. H. Kim,
Date :  11 Nov 13  (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,B,C,D  (3x)
Keywords :  Aspartyl Aminopeptidase, Tet Shape Protease, Dodecameric Peptidase, Dodecameric Tetraheral Shape, 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 Taxid: 562
    Gene: APEB, PA3247, PA3257
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1CO34Ligand/IonCARBONATE ION
2ZN8Ligand/IonZINC ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1CO312Ligand/IonCARBONATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:236 , GLU A:266 , HIS A:401 , ZN A:502 , CO3 A:503BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREHIS A:82 , ASP A:236 , ASP A:307 , ZN A:501 , CO3 A:503 , HOH A:823BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWAREHIS A:82 , ASP A:236 , GLU A:265 , GLU A:266 , ASP A:307 , HIS A:401 , ZN A:501 , ZN A:502 , HOH A:823 , HIS D:156BINDING SITE FOR RESIDUE CO3 A 503
04AC4SOFTWAREHIS B:82 , ASP B:236 , ASP B:307 , ZN B:502 , CO3 B:503 , HOH B:818BINDING SITE FOR RESIDUE ZN B 501
05AC5SOFTWAREASP B:236 , GLU B:266 , HIS B:401 , ZN B:501 , CO3 B:503BINDING SITE FOR RESIDUE ZN B 502
06AC6SOFTWAREHIS B:82 , ASP B:236 , GLU B:265 , GLU B:266 , ASP B:307 , PRO B:380 , HIS B:401 , ZN B:501 , ZN B:502 , HOH B:818 , HIS C:156BINDING SITE FOR RESIDUE CO3 B 503
07AC7SOFTWAREASP C:236 , GLU C:266 , HIS C:401 , ZN C:502 , CO3 C:503BINDING SITE FOR RESIDUE ZN C 501
08AC8SOFTWAREHIS C:82 , ASP C:236 , ASP C:307 , ZN C:501 , CO3 C:503 , HOH C:819BINDING SITE FOR RESIDUE ZN C 502
09AC9SOFTWAREHIS B:156 , HIS C:82 , ASP C:236 , GLU C:265 , GLU C:266 , ASP C:307 , HIS C:401 , ZN C:501 , ZN C:502 , HOH C:819BINDING SITE FOR RESIDUE CO3 C 503
10BC1SOFTWAREASP D:236 , GLU D:266 , HIS D:401 , ZN D:502 , CO3 D:503BINDING SITE FOR RESIDUE ZN D 501
11BC2SOFTWAREHIS D:82 , ASP D:236 , ASP D:307 , ZN D:501 , CO3 D:503 , HOH D:823BINDING SITE FOR RESIDUE ZN D 502
12BC3SOFTWAREHIS A:156 , HIS D:82 , ASP D:236 , GLU D:265 , GLU D:266 , ASP D:307 , HIS D:401 , ZN D:501 , ZN D:502 , HOH D:823BINDING SITE FOR RESIDUE CO3 D 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asp A:236 -Asn A:237
2Gly A:274 -Ala A:275
3Asp B:236 -Asn B:237
4His B:272 -Cys B:273
5Asp B:276 -Gly B:277
6Ser B:384 -Gln B:385
7Asp C:236 -Asn C:237
8Asp D:236 -Asn D:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NJR)

(-) 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:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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.hhhhh.........hhhhhhhhh.....hhhhhhhh..eeeee..ee.....hhhhh............eee.........hhhhhhhhhhhhhhh....eee........hhhhhhh....eeeee.eee......eeee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4njr A   1 MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTETGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVGAHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRAANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLDNLLSCHAGLEALLNAEGDENCILVCTDHEEVGSCSHCGADGPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADRHDANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMGIGPITASQVGVRTVDIGLPTFAMHSIRELAGSHDLAHLVKVLGAFYASSELP 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       270       280       290       300       310       320       330       340       350       360       370  ||   384       394       404       414       424     
                                                                                                                                                                                                                                                                                                                                                                                                              373|                                                   
                                                                                                                                                                                                                                                                                                                                                                                                               378                                                   


Chain B from PDB  Type:PROTEIN  Length:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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.hhhhh.........hhhhhhhhh.....hhhhhhhhh.eeeee..ee.....hhhhh............eee.........hhhhhhhhhhhhhhh....eee...................eeeee.eee......eeee.hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4njr B   1 MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTETGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVGAHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRAANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLDNLLSCHAGLEALLNAEGDENCILVCTDHEEVGSCSHCGADGPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADRHDANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMGIGPITASQVGVRTVDIGLPTFAMHSIRELAGSHDLAHLVKVLGAFYASSELP 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       270       280       290       300       310       320       330       340       350       360       370  ||   384       394       404       414       424     
                                                                                                                                                                                                                                                                                                                                                                                                              373|                                                   
                                                                                                                                                                                                                                                                                                                                                                                                               378                                                   


Chain C from PDB  Type:PROTEIN  Length:424
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..ee.............eeeeee...eeeeee....hhhhhh.eeeeee....eeeeeeeeeeee..eeeeeeeee....hhhhh...eeeeeeeeeee..eeeeeeee...........hhhhh.hhhhh...hhhhhh..eeee.......hhhhhhhhhhhhhhh....eeeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhh.......eeee.hhhhh.........hhhhhhhhh.....hhhhhhhh..eeeee..ee.....hhhhh............eee.........hhhhhhhhhhhhhhh....eee........hhhhhhhh..eeeee.eee......eeee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4njr C   1 MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTETGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVGAHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRAANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLDNLLSCHAGLEALLNAEGDENCILVCTDHEEVGSCSHCGADGPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADRHDANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMGGPITASQVGVRTVDIGLPTFAMHSIRELAGSHDLAHLVKVLGAFYASSELP 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       270       280       290       300       310       320       330       340       350       360       370  ||   385       395       405       415       425    
                                                                                                                                                                                                                                                                                                                                                                                                              373|                                                  
                                                                                                                                                                                                                                                                                                                                                                                                               379                                                  


Chain D from PDB  Type:PROTEIN  Length:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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.hhhhh.........hhhhhhhhh.....hhhhhhhh..eeeee..ee.....hhhhh............eee.........hhhhhhhhhhhhhhh....eee........hhhhhhhhh..eeeee.eee......eeee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4njr D   1 MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTETGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVGAHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRAANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLDNLLSCHAGLEALLNAEGDENCILVCTDHEEVGSCSHCGADGPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADRHDANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMGIGPITASQVGVRTVDIGLPTFAMHSIRELAGSHDLAHLVKVLGAFYASSELP 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       270       280       290       300       310       320       330       340       350       360       370  ||   384       394       404       414       424     
                                                                                                                                                                                                                                                                                                                                                                                                              373|                                                   
                                                                                                                                                                                                                                                                                                                                                                                                               378
   Legend:   → Mismatch (orange background)
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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  Cis Peptide Bonds
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    Asp B:236 - Asn B:237   [ RasMol ]  
    Asp B:276 - Gly B:277   [ RasMol ]  
    Asp C:236 - Asn C:237   [ RasMol ]  
    Asp D:236 - Asn D:237   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        APEB_PSEAE | Q9HYZ3: 2ijz 3wt4 4njq 4oid 4oiw

(-) Related Entries Specified in the PDB File

4njq COCOPAAP ASPARTYL AMINO PEPTIDASE OF PSEUDOMONAS AERUGINOSA WITH ZINC IN CATALYTIC SITE
4oid D236A MUTATION FROM ASPARTYL AMINO PEPTIDASE OF PSEUDOMONAS AERUGINOSA
4oiw