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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STREPTOMYCES GRISEUS AMINOPEPTIDASE COMPLEXED WITH L-PHENYLALANINE
 
Authors :  R. Gilboa, A. Spungin-Bialik, G. Wohlfahrt, D. Schomburg, S. Blumberg, G. Shoham
Date :  28 May 00  (Deposition) - 22 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Aminopeptidase, Double-Zinc Metalloproteinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Gilboa, A. Spungin-Bialik, G. Wohlfahrt, D. Schomburg, S. Blumberg, G. Shoham
Interactions Of Streptomyces Griseus Aminopeptidase With Amino Acid Reaction Products And Their Implications Toward A Catalytic Mechanism.
Proteins V. 44 490 2001
PubMed-ID: 11484227  |  Reference-DOI: 10.1002/PROT.1115
(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
2PHE1Mod. Amino AcidPHENYLALANINE
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:85 , ASP A:97 , ASP A:160 , ZN A:902 , PHE A:903BINDING SITE FOR RESIDUE ZN A 901
2AC2SOFTWAREASP A:97 , GLU A:132 , HIS A:247 , ZN A:901 , PHE A:903BINDING SITE FOR RESIDUE ZN A 902
3AC3SOFTWAREASP A:3 , ILE A:4 , ASP A:262 , ASP A:266 , HOH A:349 , HOH A:519BINDING SITE FOR RESIDUE CA A 905
4AC4SOFTWAREHIS A:85 , ASP A:97 , GLU A:131 , GLU A:132 , ASP A:160 , ARG A:202 , PHE A:219 , TYR A:246 , HIS A:247 , ZN A:901 , ZN A:902BINDING SITE FOR RESIDUE PHE A 903

(-) 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 1F2P)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1P_HOMO_BPS51829 P/Homo B domain profile.APX_STRGG325-445  1A:903-903

(-) Exons   (0, 0)

(no "Exon" information available for 1F2P)

(-) 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:275
 aligned with APX_STRGG | P80561 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:289
                                    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         
            APX_STRGG    46 APDIPLANVKAHLTQLSTIAANNGGNRAHGRPGYKASVDYVKAKLDAAGYTTTLQQFTSGGATGYNLIADWPGGDPNKVLMAGAHLDSVSSGAGINDNGSGSAAVLETALAVSRAGYQPDKHLRFAWWGAEELGLIGSKYYVNNLPSADRSKLAGYLNFDMIGSPNPGYFVYDDDPVIEKTFKDYFAGLNVPTEIETEGDGRSDHAPFKNVGVPVGGLFTGAGYTKSAAQAQKWGGTAGQAFDRCYHSSCDSLSNINDTALDRNSDAAAHAIWTLSSGTGEPPTGEGVF 334
               SCOP domains d1f2pa_ A: Aminopeptidase                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1f2pA00 A:1-277 Zn peptidases                                                                                                                                                                                                                                                                   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeeeee....eeeeeeeeeee............hhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..........ee...hhhhhhhhhhhhhhh....ee...---...hhhhhh....eeeee.......hhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhh-----------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P_HOMO_B   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f2p A   1 APDIPLANVKAHLTQLSTIAANNGGNRAHGRPGYKASVDYVKAKLDAAGYTTTLQQFTSGGATGYNLIANWPGGDPNKVLMAGAHLDSVSSGAGINDNGSGSAAVLETALAVSRAGYQPDKHLRFAWWGAEELGLIGSKFYVNNLPSADRSKLAGYLNFDMIGSPNPGYFVYDDDPVIEKTFKNYFAGLNVPTEIETE---RSDHAPFKNVGVPVGGLFTGAGYTKSAAQAQKWGGTAGQAFDRCYHSSCDSLSNINDTALDRNSDAAAHAIWTLSS-----------F 903
                                    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      |  -        |
                                                                                                                                                                                                                               198 202                                                                        277         903
   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 1F2P)

(-) 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 1qq9 1tf8 1tf9 1tkf 1tkh 1tkj 1xbu 1xjo

(-) Related Entries Specified in the PDB File

1cp7 1CP7 CONTAINS THE NATIVE FORM OF THE SAME PROTEIN
1f2o 1F2O CONTAINS THE SAME PROTEIN COMPLEXED WITH L-LEUCINE
1qq9 1QQ9 CONTAINS THE SAME PROTEIN COMPLEXED WITH L-METHIONINE
1xjo 1XJO CONTAINS THE NATIVE FORM OF THE SAME PROTEIN