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(-) Description

Title :  CRYSTAL STRUCTURE OF TETRAHEDRAL AMINOPEPTIDASE FROM P. HORIKOSHII IN COMPLEX WITH AMASTATIN
 
Authors :  M. Groll, L. Borissenko
Date :  16 Nov 04  (Deposition) - 01 Mar 05  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (12x)
Keywords :  Aminopeptidase, Pdz, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Borissenko, M. Groll
Crystal Structure Of Tet Protease Reveals Complementary Protein Degradation Pathways In Prokaryotes
J. Mol. Biol. V. 346 1207 2005
PubMed-ID: 15713475  |  Reference-DOI: 10.1016/J.JMB.2004.12.056

(-) Compounds

Molecule 1 - FRV OPERON PROTEIN FRVX
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET 6C
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
 
Molecule 2 - AMASTATIN
    Chains: B
    Engineered: YES
    Organism Scientific: STREPTOMYCES SP. ME98-M3
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (12x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1L2O1Mod. Amino Acid(2S,3R)-3-AMINO-2-HYDROXY-5-METHYLHEXANOIC ACID
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1L2O12Mod. Amino Acid(2S,3R)-3-AMINO-2-HYDROXY-5-METHYLHEXANOIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:68 , ASP A:182 , ASP A:235 , ZN A:1002 , L2O B:1BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWAREASP A:182 , GLU A:213 , HIS A:323 , ZN A:1001 , L2O B:1BINDING SITE FOR RESIDUE ZN A 1002
3AC3SOFTWAREHIS A:68 , ASP A:182 , GLU A:212 , GLU A:213 , ASP A:235 , VAL A:236 , LEU A:293 , GLY A:296 , GLY A:297 , ILE A:322 , HIS A:323 , ZN A:1001 , ZN A:1002 , HOH B:101BINDING SITE FOR CHAIN B OF AMASTATIN

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y0Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y0Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y0Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y0Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y0Y)

(-) 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:335
 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 d1y0ya3 A:6-72,A:164-351 Frv operon protein FrvX, catalytic domain d1y0ya1 A:73-163 Frv operon protein FrvX                                                   d1y0ya3 A:6-72,A:164-351 Frv operon protein FrvX, catalytic domain                                                                                                                          -- SCOP domains
               CATH domains 1y0yA01 A:6-71,A:166-353 Zn peptidases                            1y0yA02 A:72-165 Aminopeptidase/glucanase lid do             main; domain 2                   1y0yA01 A:6-71,A:166-353 Zn peptidases                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------Peptidase_M42-1y0yA01 A:50-340                                                                                                                                                                                                                                                                     ------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.eeee.....eeeee.....eeeeeee....eeeeeee.....eeeeee...hhhhh...eeeeeee..eeeeeeee.-------------..hhhhheee....hhhhhhhh......eeee....eee...eeee.hhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhh..eeeeeeeee.......hhhhh.......eeeeeee..ee.hhhhhhhhhhhhhhh...eeeee......hhhhhh.......eeeeeeee.......eeeehhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y0y A   6 MVDYELLKKVVEAPGVSGYEFLGIRDVVIEEIKDYVDEVKVDKLGNVIAHKKGEGPKVMIAAHMDQIGLMVTHIEKNGFLRVAPIGGVDPKTLIAQRFKVWIDKGKFIYGVGAS-------------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        
                                                                                                                                           119           133                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 1y0y B   1 xVVD   4
                            |   
                            1-L2O
   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  (2, 2)

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

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Peptidase_MH (119)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1vhe CRYSTAL STRUCTURE OF A AMINOPEPTIDASE/GLUCANASE HOMOLOG
1vho CRYSTAL STRUCTURE OF A PUTATIVE PEPTIDASE/ENDOGLUCANASE
1xfo CRYSTAL STRUCTURE OF FRVX
1y0r CRYSTAL STRUCTURE OF TET FROM P. HORIKOSHII, NATIVE