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(-) Description

Title :  ZN SUBSTITUTED E.COLI AMINOPEPTIDASE P IN COMPLEX WITH PRODUCT
 
Authors :  S. C. Graham, C. S. Bond, H. C. Freeman, J. M. Guss
Date :  07 Jan 05  (Deposition) - 29 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Hydrolase, Proline-Specific Peptidase, Product Complex, Metalloenzyme, Pita-Bread Fold, Dinuclear Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Graham, C. S. Bond, H. C. Freeman, J. M. Guss
Structural And Functional Implications Of Metal Ion Selection In Aminopeptidase P, A Metalloprotease With A Dinuclear Metal Center.
Biochemistry V. 44 13820 2005
PubMed-ID: 16229471  |  Reference-DOI: 10.1021/BI0512849

(-) Compounds

Molecule 1 - XAA-PRO AMINOPEPTIDASE
    Chains: A
    EC Number: 3.4.11.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPL670
    Expression System Strain: AN1459
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: DIPEPTIDE PRODUCT OF AMINOPEPTIDASE P (FORMED BY CLEVAGE OF XAA-PRO-LEU TRIPEPTIDE SUBSTRATE)
    Strain: AN1459
    Synonym: AMINOPEPTIDASE P, X-PRO AMINOPEPTIDASE, APP-II, AMINOPEPTIDASE P II, AMINOACYLPROLINE AMINOPEPTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric Unit (5, 8)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2LEU1Mod. Amino AcidLEUCINE
3MG1Ligand/IonMAGNESIUM ION
4PRO1Mod. Amino AcidPROLINE
5ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1FLC4Ligand/IonCITRATE ANION
2LEU4Mod. Amino AcidLEUCINE
3MG-1Ligand/IonMAGNESIUM ION
4PRO4Mod. Amino AcidPROLINE
5ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:229 , ASP A:260 , ASP A:271 , THR A:273 , GLU A:406 , ZN A:1002 , HOH A:2145BINDING SITE FOR RESIDUE ZN A1001
2AC2SOFTWAREASP A:271 , HIS A:354 , THR A:381 , GLU A:383 , GLU A:406 , ZN A:1001 , HOH A:2145BINDING SITE FOR RESIDUE ZN A1002
3AC3SOFTWAREARG A:186 , MET A:193 , ARG A:221 , HIS A:222BINDING SITE FOR RESIDUE FLC A1005
4AC4SOFTWAREHIS A:71BINDING SITE FOR RESIDUE ZN A1007
5AC5SOFTWAREHIS A:243 , HIS A:361 , PRO A:501 , HOH A:2146BINDING SITE FOR RESIDUE ZN A1008
6AC6SOFTWAREARG A:399 , HOH A:2087 , HOH A:2089 , HOH A:2091 , HOH A:2131 , HOH A:2132 , HOH A:2133BINDING SITE FOR RESIDUE MG A1003
7AC7SOFTWAREHIS A:243 , ASP A:260 , HIS A:350 , HIS A:361 , GLU A:383 , ARG A:404 , LEU A:502 , ZN A:1008 , HOH A:2145BINDING SITE FOR RESIDUE PRO A 501
8AC8SOFTWARETRP A:88 , ARG A:153 , GLY A:351 , TYR A:366 , ARG A:370 , PRO A:501 , HOH A:2117BINDING SITE FOR RESIDUE LEU A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BH3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BH3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BH3)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROLINE_PEPTIDASEPS00491 Aminopeptidase P and proline dipeptidase signature.AMPP_ECOLI351-363  1A:350-362
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROLINE_PEPTIDASEPS00491 Aminopeptidase P and proline dipeptidase signature.AMPP_ECOLI351-363  4A:350-362

(-) Exons   (0, 0)

(no "Exon" information available for 2BH3)

(-) 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:442
 aligned with AMPP_ECOLI | P15034 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:442
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 441  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441  
           AMPP_ECOLI     2 SEISRQEFQRRRQALVEQMQPGSAALIFAAPEVTRSADSEYPYRQNSDFWYFTGFNEPEAVLVLIKSDDTHNHSVLFNRVRDLTAEIWFGRRLGQDAAPEKLGVDRALAFSEINQQLYQLLNGLDVVYHAQGEYAYADVIVNSALEKLRKGSRQNLTAPATMIDWRPVVHEMRLFKSPEEIAVLRRAGEITAMAHTRAMEKCRPGMFEYHLEGEIHHEFNRHGARYPSYNTIVGSGENGCILHYTENECEMRDGDLVLIDAGCEYKGYAGDITRTFPVNGKFTQAQREIYDIVLESLETSLRLYRPGTSILEVTGEVVRIMVSGLVKLGILKGDVDELIAQNAHRPFFMHGLSHWLGLDVHDVGVYGQDRSRILEPGMVLTVEPGLYIAPDAEVPEQYRGIGIRIEDDIVITETGNENLTASVVKKPEEIEALMVAARKQ--   -
               SCOP domains d2bh3a1 A:1-176 Aminopeptidase P                                                                                                                                                d2bh3a2 A:177-440 Aminopeptidase P, C-terminal domain                                                                                                                                                                                                                   -- SCOP domains
               CATH domains 2bh3A01 A:1-173 Creatine Amidinohydrolase, subunit A, domain 1                                                                                                               2bh3A02 A:174-440 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                                         -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeee.....eee..ee.....hhhhhhhhh......eeeeee.....eeeeeee...hhhhhhhhh......hhhhhhh..eeee..hhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...ee....eeee.hhhhh..............eeeeee.eee..ee..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.........................hhhhh.......eeee..eeee......hhhhh.eeee..eeeee....eee.......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PROLINE_PEPTI-------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bh3 A   1 SEISRQEFQRRRQALVEQMQPGSAALIFAAPEVTRSADSEYPYRQNSDFWYFTGFNEPEAVLVLIKSDDTHNHSVLFNRVRDLTAEIWFGRRLGQDAAPEKLGVDRALAFSEINQQLYQLLNGLDVVYHAQGEYAYADVIVNSALEKLRKGSRQNLTAPATMIDWRPVVHEMRLFKSPEEIAVLRRAGEITAMAHTRAMEKCRPGMFEYHLEGEIHHEFNRHGARYPSYNTIVGSGENGCILHYTENECEMRDGDLVLIDAGCEYKGYAGDITRTFPVNGKFTQAQREIYDIVLESLETSLRLYRPGTSILEVTGEVVRIMVSGLVKLGILKGDVDELIAQNAHRPFFMHGLSHWLGLDVHDVGVYGQDRSRILEPGMVLTVEPGLYIAPDAEVPEQYRGIGIRIEDDIVITETGNENLTASVVKKPEEIEALMVAARKQPL 502
                                    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       380       390       400       410       420       430       440| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 440| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  501
   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: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BH3)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (AMPP_ECOLI | P15034)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008235    metalloexopeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain 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: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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMPP_ECOLI | P15034: 1a16 1jaw 1m35 1n51 1w2m 1w7v 1wbq 1wl6 1wl9 1wlr 2bha 2bhb 2bhc 2bhd 2bn7 2bws 2bwt 2bwu 2bwv 2bww 2bwx 2bwy 2v3x 2v3y 2v3z

(-) Related Entries Specified in the PDB File

1a16 AMINOPEPTIDASE P FROM E. COLI WITH THE INHIBITOR PRO-LEU
1jaw AMINOPEPTIDASE P FROM E. COLI LOW PH FORM
1m35 AMINOPEPTIDASE P FROM ESCHERICHIA COLI
1n51 AMINOPEPTIDASE P IN COMPLEX WITH THE INHIBITOR APSTATIN
1w2m CA-SUBSTITUTED FORM OF E. COLI AMINOPEPTIDASE P
1w7v ZNMG SUBSTRITUTED AMINOPEPTIDASE P FROM E. COLI
1wbq ZNMG SUBSTITUTED AMINOPEPTIDASE P FROM E. COLI
1wl6 MG-SUBSTITUTED FORM OF E. COLI AMINOPEPTIDASE P
1wl9 STRUCTURE OF AMINOPEPTIDASE P FROM E. COLI
1wlr APO AMINOPEPTIDASE P FROM E. COLI
2bha E. COLI AMINOPEPTIDASE P IN COMPLEX WITH SUBSTRATE
2bhb ZN SUBSTITUTED E. COLI AMINOPEPTIDASE P
2bhc NA SUBSTITUTED E. COLI AMINOPEPTIDASE P
2bhd MG SUBSTITUTED E. COLI AMINOPEPTIDASE P IN COMPLEX WITH A PRODUCT-LIKE INHIBITOR
2bn7 MN SUBSTITUTED E. COLI AMINOPEPTIDASE P IN COMPLEX WITH PRODUCT AND ZN
2bws HIS243ALA E. COLI AMINOPEPTIDASE P
2bwt ASP260ALA E. COLI AMINOPEPTIDASE P
2bwu ASP271ALA E. COLI AMINOPEPTIDASE P
2bwv HIS361ALA E. COLI AMINOPEPTIDASE P
2bww HIS350ALA E. COLI AMINOPEPTIDASE P
2bwx HIS354ALA E. COLI AMINOPEPTIDASE P
2bwy GLU383ALA E. COLI AMINOPEPTIDASE P