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(-) Description

Title :  STREPTOMYCES GRISEUS AMINOPEPTIDASE COMPLEXED WITH D-TRYPTOPHAN
 
Authors :  V. Reiland, R. Gilboa, A. Spungin-Bialik, D. Schomburg, Y. Shoham, S. Blumberg, G. Shoham
Date :  08 Jun 04  (Deposition) - 14 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Double-Zinc Metalloproteinase, Calcium Activation, Protein- Inhibitor Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Reiland, R. Gilboa, A. Spungin-Bialik, D. Schomburg, Y. Shoham, S. Blumberg, G. Shoham
Interactions Of D Amino Acids With Streptomyces Griseus Aminopeptidase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMINOPEPTIDASE
    Chains: A
    EC Number: 3.4.11.-
    Organism Scientific: STREPTOMYCES GRISEUS
    Organism Taxid: 1911
    Other Details: THE ENZYME IS ISOLATED FROM THE COMMERCIALLY AVAILABLE ENZYME MIXTURE "PRONASE E".
    Synonym: SGAP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2DTR1Ligand/IonD-TRYPTOPHAN
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:85 , ASP A:97 , ASP A:160 , ZN A:902 , DTR A:913BINDING SITE FOR RESIDUE ZN A 901
2AC2SOFTWAREASP A:97 , GLU A:132 , HIS A:247 , ZN A:901 , DTR A:913BINDING SITE FOR RESIDUE ZN A 902
3AC3SOFTWAREASP A:3 , ILE A:4 , ASP A:262 , ASP A:266 , HOH A:1292 , HOH A:1414BINDING SITE FOR RESIDUE CA A 905
4AC4SOFTWAREHIS A:85 , ASP A:97 , GLU A:132 , ASP A:160 , MET A:161 , TYR A:172 , GLU A:196 , ARG A:202 , PHE A:219 , TYR A:246 , HIS A:247 , ZN A:901 , ZN A:902 , HOH A:1236 , HOH A:1263BINDING SITE FOR RESIDUE DTR A 913

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:245 -A:250

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:97 -Asn A:98

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1TKF)

(-) 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:273
 aligned with APX_STRGG | P80561 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:277
                                    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       
            APX_STRGG    46 APDIPLANVKAHLTQLSTIAANNGGNRAHGRPGYKASVDYVKAKLDAAGYTTTLQQFTSGGATGYNLIADWPGGDPNKVLMAGAHLDSVSSGAGINDNGSGSAAVLETALAVSRAGYQPDKHLRFAWWGAEELGLIGSKYYVNNLPSADRSKLAGYLNFDMIGSPNPGYFVYDDDPVIEKTFKDYFAGLNVPTEIETEGDGRSDHAPFKNVGVPVGGLFTGAGYTKSAAQAQKWGGTAGQAFDRCYHSSCDSLSNINDTALDRNSDAAAHAIWTLSS 322
               SCOP domains d1tkfa_ A: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1tkfA00 A:1-277 Zn peptidases                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeeeee....eeeeeeeeeee............hhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..........eee..hhhhhhhhhhhhhhh....eee----...hhhhhhh....eeeee.......hhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tkf A   1 APDIPLANVKAHLTQLSTIAANNGGNRAHGRPGYKASVDYVKAKLDAAGYTTTLQQFTSGGATGYNLIANWPGGDPNKVLMAGAHLDSVSSGAGINDNGSGSAAVLETALAVSRAGYQPDKHLRFAWWGAEELGLIGSKFYVNNLPSADRSKLAGYLNFDMIGSPNPGYFVYDDDPVIEKTFKNYFAGLNVPTEIE----GRSDHAPFKNVGVPVGGLFTGAGYTKSAAQAQKWGGTAGQAFDRCYHSSCDSLSNINDTALDRNSDAAAHAIWTLSS 277
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     |   -|      210       220       230       240       250       260       270       
                                                                                                                                                                                                                             196  201
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1TKF)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (APX_STRGG | P80561)
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: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.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        APX_STRGG | P80561: 1cp7 1f2o 1f2p 1qq9 1tf8 1tf9 1tkh 1tkj 1xbu 1xjo

(-) Related Entries Specified in the PDB File

1cp7 NATIVE FORM OF THE SAME PROTEIN
1f2o THE SAME PROTEIN COMPLEXED WITH L-LEUCINE
1f2p THE SAME PROTEIN COMPLEXED WITH L-PHENYLALANINE
1qq9 THE SAME PROTEIN COMPLEXED WITH L-METHIONINE
1tf8 THE SAME PROTEIN COMPLEXED WITH L-TRYPTOPHAN
1tf9 THE SAME PROTEIN COMPLEXED WITH P-IODO-L-PHENYLALANINE
1tkh THE SAME PROTEIN COMPLEXED WITH D-PHENYLALANINE
1tkj THE SAME PROTEIN COMPLEXED WITH D-METHIONINE
1xjo NATIVE FORM OF THE SAME PROTEIN