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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ARCHAEAL AMINOPEPTIDASE
 
Authors :  S. Russo, U. Baumann
Date :  15 Sep 04  (Deposition) - 05 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Aminopeptidase, Self-Compartmentalizing, Metalloprotease, Dinuclear, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Russo, U. Baumann
Crystal Structure Of A Dodecameric Tetrahedral Shaped Aminopeptidase
J. Biol. Chem. V. 279 51275 2004
PubMed-ID: 15375159  |  Reference-DOI: 10.1074/JBC.M409455200

(-) Compounds

Molecule 1 - FRV OPERON PROTEIN FRVX
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: FRVX AMINOPEPTIDASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS C:68 , ASP C:182 , ASP C:235 , ZN C:355 , HOH C:415BINDING SITE FOR RESIDUE ZN C 354
2AC2SOFTWAREHIS A:68 , ASP A:182 , ASP A:235 , ZN A:382 , HOH A:465BINDING SITE FOR RESIDUE ZN A 354
3AC3SOFTWAREHIS D:68 , ASP D:182 , ASP D:235 , ZN D:355 , HOH D:435BINDING SITE FOR RESIDUE ZN D 354
4AC4SOFTWAREASP D:182 , GLU D:213 , HIS D:323 , ZN D:354 , HOH D:435BINDING SITE FOR RESIDUE ZN D 355
5AC5SOFTWAREASP C:182 , GLU C:213 , HIS C:323 , ZN C:354 , HOH C:415BINDING SITE FOR RESIDUE ZN C 355
6AC6SOFTWAREASP B:182 , GLU B:213 , HIS B:323 , ZN B:371 , HOH B:426BINDING SITE FOR RESIDUE ZN B 354
7AC7SOFTWAREHIS B:68 , ASP B:182 , ASP B:235 , ZN B:354 , HOH B:426BINDING SITE FOR RESIDUE ZN B 371
8AC8SOFTWAREASP A:182 , GLU A:213 , HIS A:323 , ZN A:354 , HOH A:465BINDING SITE FOR RESIDUE ZN A 382

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:182 -Asp A:183
2Asp B:182 -Asp B:183
3Asp C:182 -Asp C:183
4Asp D:182 -Asp D:183

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XFO)

(-) 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:346
 aligned with TET_PYRHO | O59196 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:357
                                1                                                                                                                                                                                                                                                                                                                                                                
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       
            TET_PYRHO     - ----MEVRNMVDYELLKKVVEAPGVSGYEFLGIRDVVIEEIKDYVDEVKVDKLGNVIAHKKGEGPKVMIAAHMDQIGLMVTHIEKNGFLRVAPIGGVDPKTLIAQRFKVWIDKGKFIYGVGASVPPHIQKPEDRKKAPDWDQIFIDIGAESKEEAEDMGVKIGTVITWDGRLERLGKHRFVSIAFDDRIAVYTILEVAKQLKDAKADVYFVATVQEEVGLRGARTSAFGIEPDYGFAIDVTIAADIPGTPEHKQVTHLGKGTAIKIMDRSVICHPTIVRWLEELAKKHEIPYQLEILLGGGTDAGAIHLTKAGVPTGALSVPARYIHSNTEVVDERDVDATVELMTKALENIHELKI 353
               SCOP domains ---------d1xfoa2 A:6-72,A:164-353 Frv operon protein FrvX, catalytic domain d1xfoa1 A:73-163 Frv operon protein FrvX                                                   d1xfoa2 A:6-72,A:164-353 Frv operon protein FrvX, catalytic domain                                                                                                                             SCOP domains
               CATH domains 1xfoA01 A:-3-71,A:166-353 Zn peptidases                                    1xfoA02 A:72-165 Aminopeptidase/glucanase lid doma           in; domain 2                     1xfoA01 A:-3-71,A:166-353 Zn peptidases                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.eeee.....eeeee.....eeeeeee....eeeeeee.....eeeeee...hhhhh...eeeeeee..eeeeeeeee..-----------..hhh.eeee....hhhhhhhh......eeee....eee...eeee.hhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhh..eeeeeeeee.......hhhhh.......eeeeee......hhhhhhhhhhhhhhh...eeeee......hhhhhh.......eeeeeeee.......eeeehhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xfo A  -3 RGSHMEVRNMVDYELLKKVVEAPGVSGYEFLGIRDVVIEEIKDYVDEVKVDKLGNVIAHKKGEGPKVMIAAHMDQIGLMVTHIEKNGFLRVAPIGGVDPKTLIAQRFKVWIDKGKFIYGVGASVP-----------APDWDQIFIDIGAESKEEAEDMGVKIGTVITWDGRLERLGKHRFVSIAFDDRIAVYTILEVAKQLKDAKADVYFVATVQEEVGLRGARTSAFGIEPDYGFAIDVTIAADIPGTPEHKQVTHLGKGTAIKIMDRSVICHPTIVRWLEELAKKHEIPYQLEILLGGGTDAGAIHLTKAGVPTGALSVPARYIHSNTEVVDERDVDATVELMTKALENIHELKI 353
                                     6        16        26        36        46        56        66        76        86        96       106       116    |    -      |136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       
                                                                                                                                                      121         133                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:337
 aligned with TET_PYRHO | O59196 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:348
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345        
            TET_PYRHO     6 MVDYELLKKVVEAPGVSGYEFLGIRDVVIEEIKDYVDEVKVDKLGNVIAHKKGEGPKVMIAAHMDQIGLMVTHIEKNGFLRVAPIGGVDPKTLIAQRFKVWIDKGKFIYGVGASVPPHIQKPEDRKKAPDWDQIFIDIGAESKEEAEDMGVKIGTVITWDGRLERLGKHRFVSIAFDDRIAVYTILEVAKQLKDAKADVYFVATVQEEVGLRGARTSAFGIEPDYGFAIDVTIAADIPGTPEHKQVTHLGKGTAIKIMDRSVICHPTIVRWLEELAKKHEIPYQLEILLGGGTDAGAIHLTKAGVPTGALSVPARYIHSNTEVVDERDVDATVELMTKALENIHELKI 353
               SCOP domains d1xfob2 B:6-72,B:164-353 Frv operon protein FrvX, catalytic domain d1xfob1 B:73-163 Frv operon protein FrvX                                                   d1xfob2 B:6-72,B:164-353 Frv operon protein FrvX, catalytic domain                                                                                                                             SCOP domains
               CATH domains 1xfoB01 B:6-71,B:166-353 Zn peptidases                            1xfoB02 B:72-165 Aminopeptidase/glucanase lid doma           in; domain 2                     1xfoB01 B:6-71,B:166-353 Zn peptidases                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.eeee.....eeeee.....eeeeeee....eeeeeee.....eeeeee...hhhhh...eeeeeee..eeeeeeeee..-----------..hhh.eeee....hhhhhhhh......eeee....eee...eeee.hhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhh..eeeeeeeee.......hhhhh.......eeeeeee..ee.hhhhhhhhhhhhhhhh..eeeee......hhhhhh.......eeeeeeeee......eeeehhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xfo B   6 MVDYELLKKVVEAPGVSGYEFLGIRDVVIEEIKDYVDEVKVDKLGNVIAHKKGEGPKVMIAAHMDQIGLMVTHIEKNGFLRVAPIGGVDPKTLIAQRFKVWIDKGKFIYGVGASVP-----------APDWDQIFIDIGAESKEEAEDMGVKIGTVITWDGRLERLGKHRFVSIAFDDRIAVYTILEVAKQLKDAKADVYFVATVQEEVGLRGARTSAFGIEPDYGFAIDVTIAADIPGTPEHKQVTHLGKGTAIKIMDRSVICHPTIVRWLEELAKKHEIPYQLEILLGGGTDAGAIHLTKAGVPTGALSVPARYIHSNTEVVDERDVDATVELMTKALENIHELKI 353
                                    15        25        35        45        55        65        75        85        95       105       115     |   -       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345        
                                                                                                                                             121         133                                                                                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:337
 aligned with TET_PYRHO | O59196 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:348
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345        
            TET_PYRHO     6 MVDYELLKKVVEAPGVSGYEFLGIRDVVIEEIKDYVDEVKVDKLGNVIAHKKGEGPKVMIAAHMDQIGLMVTHIEKNGFLRVAPIGGVDPKTLIAQRFKVWIDKGKFIYGVGASVPPHIQKPEDRKKAPDWDQIFIDIGAESKEEAEDMGVKIGTVITWDGRLERLGKHRFVSIAFDDRIAVYTILEVAKQLKDAKADVYFVATVQEEVGLRGARTSAFGIEPDYGFAIDVTIAADIPGTPEHKQVTHLGKGTAIKIMDRSVICHPTIVRWLEELAKKHEIPYQLEILLGGGTDAGAIHLTKAGVPTGALSVPARYIHSNTEVVDERDVDATVELMTKALENIHELKI 353
               SCOP domains d1xfoc2 C:6-72,C:164-353 Frv operon protein FrvX, catalytic domain d1xfoc1 C:73-163 Frv operon protein FrvX                                                   d1xfoc2 C:6-72,C:164-353 Frv operon protein FrvX, catalytic domain                                                                                                                             SCOP domains
               CATH domains 1xfoC01 C:6-71,C:166-353 Zn peptidases                            1xfoC02 C:72-165 Aminopeptidase/glucanase lid doma           in; domain 2                     1xfoC01 C:6-71,C:166-353 Zn peptidases                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.eeee.....eeeee.....eeeeeee....eeeeeee.....eeeeee...hhhhh...eeeeeee..eeeeeeeee..-----------..hhh.eeee....hhhhhhhh......eeee....eee...eeee.hhhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeee.......hhhhh.......eeeeee......hhhhhhhhhhhhhhh...eeeee......hhhhhh.......eeeeeeeee......eeeehhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xfo C   6 MVDYELLKKVVEAPGVSGYEFLGIRDVVIEEIKDYVDEVKVDKLGNVIAHKKGEGPKVMIAAHMDQIGLMVTHIEKNGFLRVAPIGGVDPKTLIAQRFKVWIDKGKFIYGVGASVP-----------APDWDQIFIDIGAESKEEAEDMGVKIGTVITWDGRLERLGKHRFVSIAFDDRIAVYTILEVAKQLKDAKADVYFVATVQEEVGLRGARTSAFGIEPDYGFAIDVTIAADIPGTPEHKQVTHLGKGTAIKIMDRSVICHPTIVRWLEELAKKHEIPYQLEILLGGGTDAGAIHLTKAGVPTGALSVPARYIHSNTEVVDERDVDATVELMTKALENIHELKI 353
                                    15        25        35        45        55        65        75        85        95       105       115     |   -       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345        
                                                                                                                                             121         133                                                                                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:337
 aligned with TET_PYRHO | O59196 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:348
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345        
            TET_PYRHO     6 MVDYELLKKVVEAPGVSGYEFLGIRDVVIEEIKDYVDEVKVDKLGNVIAHKKGEGPKVMIAAHMDQIGLMVTHIEKNGFLRVAPIGGVDPKTLIAQRFKVWIDKGKFIYGVGASVPPHIQKPEDRKKAPDWDQIFIDIGAESKEEAEDMGVKIGTVITWDGRLERLGKHRFVSIAFDDRIAVYTILEVAKQLKDAKADVYFVATVQEEVGLRGARTSAFGIEPDYGFAIDVTIAADIPGTPEHKQVTHLGKGTAIKIMDRSVICHPTIVRWLEELAKKHEIPYQLEILLGGGTDAGAIHLTKAGVPTGALSVPARYIHSNTEVVDERDVDATVELMTKALENIHELKI 353
               SCOP domains d1xfod2 D:6-72,D:164-353 Frv operon protein FrvX, catalytic domain d1xfod1 D:73-163 Frv operon protein FrvX                                                   d1xfod2 D:6-72,D:164-353 Frv operon protein FrvX, catalytic domain                                                                                                                             SCOP domains
               CATH domains 1xfoD01 D:6-71,D:166-353 Zn peptidases                            1xfoD02 D:72-165 Aminopeptidase/glucanase lid doma           in; domain 2                     1xfoD01 D:6-71,D:166-353 Zn peptidases                                                                                                                                                       CATH domains
           Pfam domains (1) --------------------------------------------Peptidase_M42-1xfoD01 D:50-340                                                                                                                                                                                                                                                                     ------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------Peptidase_M42-1xfoD02 D:50-340                                                                                                                                                                                                                                                                     ------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------Peptidase_M42-1xfoD03 D:50-340                                                                                                                                                                                                                                                                     ------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------Peptidase_M42-1xfoD04 D:50-340                                                                                                                                                                                                                                                                     ------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.eeee.....eeeee.....eeeeeee....eeeeeee.....eeeeee...hhhhh...eeeeeee..eeeeeeeee..-----------..hhh.eeee....hhhhhhhh......eeee....eee...eeee.hhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhh..eeeeeeeee.......hhhhh.......eeeeee......hhhhhhhhhhhhhhh...eeeee......hhhhhh.......eeeeeeee.......eeeehhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xfo D   6 MVDYELLKKVVEAPGVSGYEFLGIRDVVIEEIKDYVDEVKVDKLGNVIAHKKGEGPKVMIAAHMDQIGLMVTHIEKNGFLRVAPIGGVDPKTLIAQRFKVWIDKGKFIYGVGASVP-----------APDWDQIFIDIGAESKEEAEDMGVKIGTVITWDGRLERLGKHRFVSIAFDDRIAVYTILEVAKQLKDAKADVYFVATVQEEVGLRGARTSAFGIEPDYGFAIDVTIAADIPGTPEHKQVTHLGKGTAIKIMDRSVICHPTIVRWLEELAKKHEIPYQLEILLGGGTDAGAIHLTKAGVPTGALSVPARYIHSNTEVVDERDVDATVELMTKALENIHELKI 353
                                    15        25        35        45        55        65        75        85        95       105       115     |   -       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345        
                                                                                                                                             121         133
   Legend:   → Mismatch (orange background)
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    → 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  (2, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Topology: Aminopeptidase (284)
(-)
Homologous Superfamily: Zn peptidases (137)
(-)
Pyrococcus horikoshii. Organism_taxid: 53953. (4)
1a1xfoA01A:-3-71,A:166-353
1b1xfoB01B:6-71,B:166-353
1c1xfoC01C:6-71,C:166-353
1d1xfoD01D:6-71,D:166-353
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Peptidase_MH (119)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TET_PYRHO | O59196)
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:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds 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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  1xfo
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  TET_PYRHO | O59196
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 Related Entries

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

UniProtKB/Swiss-Prot
        TET_PYRHO | O59196: 1y0r 1y0y

(-) Related Entries Specified in the PDB File

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