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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI AMINOPEPTIDASE N IN COMPLEX WITH L-SERINE
 
Authors :  A. Addlagatta, R. Gumpena, C. Kishor, R. J. Ganji
Date :  31 Jan 11  (Deposition) - 16 Nov 11  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Thermolysin Like Catalytic Domain, Hydrolase, L-Serine Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Gumpena, C. Kishor, R. J. Ganji, A. Addlagatta
Discovery Of Alpha, Beta- And Alpha, Gamma-Diamino Acid Scaffolds For The Inhibition Of M1 Family Aminopeptidases
Chemmedchem V. 6 1971 2011
PubMed-ID: 22025387  |  Reference-DOI: 10.1002/CMDC.201100298

(-) Compounds

Molecule 1 - AMINOPEPTIDASE N
    Chains: A
    EC Number: 3.4.11.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B0932, JW0915, K-12, PEPN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: ALPHA-AMINOACYLPEPTIDE HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric/Biological Unit (5, 19)
No.NameCountTypeFull Name
1GOL13Ligand/IonGLYCEROL
2MLI1Ligand/IonMALONATE ION
3NA3Ligand/IonSODIUM ION
4SER1Mod. Amino AcidSERINE
5ZN1Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:297 , HIS A:301 , GLU A:320 , SER A:900BINDING SITE FOR RESIDUE ZN A 880
02AC2SOFTWARESER A:332 , ASP A:333 , GLY A:335 , HOH A:1444 , HOH A:1643 , HOH A:1689BINDING SITE FOR RESIDUE NA A 890
03AC3SOFTWAREASP A:452 , HOH A:1288 , HOH A:1289 , HOH A:1640BINDING SITE FOR RESIDUE NA A 891
04AC4SOFTWAREMET A:260 , ASN A:373 , GLN A:821 , HOH A:1506 , HOH A:1530 , HOH A:1574BINDING SITE FOR RESIDUE NA A 892
05AC5SOFTWAREGLU A:121 , MET A:260 , ALA A:262 , GLU A:264 , HIS A:297 , GLU A:298 , HIS A:301 , LYS A:319 , GLU A:320 , TYR A:381 , ZN A:880 , GOL A:976 , HOH A:1425 , HOH A:1638BINDING SITE FOR RESIDUE SER A 900
06AC6SOFTWAREARG A:641 , GLU A:642 , THR A:645 , ARG A:686 , PHE A:690 , ALA A:722 , HOH A:1029 , HOH A:1432 , HOH A:1573BINDING SITE FOR RESIDUE MLI A 950
07AC7SOFTWARELEU A:532 , TRP A:546 , ASP A:566 , ALA A:567 , SER A:570 , HOH A:965BINDING SITE FOR RESIDUE GOL A 970
08AC8SOFTWARETYR A:376 , THR A:377 , TYR A:381 , GLU A:382 , ARG A:825 , GOL A:982 , HOH A:1638 , HOH A:1705BINDING SITE FOR RESIDUE GOL A 971
09AC9SOFTWARETRP A:71 , THR A:72 , TRP A:74 , ARG A:669 , VAL A:670 , GLU A:671 , GOL A:973 , HOH A:1515 , HOH A:1794BINDING SITE FOR RESIDUE GOL A 972
10BC1SOFTWARELEU A:61 , VAL A:62 , TRP A:74 , ARG A:669 , GLU A:671 , GOL A:972 , HOH A:1794BINDING SITE FOR RESIDUE GOL A 973
11BC2SOFTWAREHIS A:11 , GLN A:467 , ARG A:468 , THR A:469 , LYS A:478 , GLN A:479 , PRO A:480 , ALA A:515 , HOH A:1115 , HOH A:1373 , HOH A:1491BINDING SITE FOR RESIDUE GOL A 974
12BC3SOFTWAREGLU A:292 , VAL A:670 , HIS A:672 , HOH A:1390 , HOH A:1565BINDING SITE FOR RESIDUE GOL A 975
13BC4SOFTWAREGLY A:261 , ARG A:293 , HIS A:297 , TYR A:381 , SER A:900 , GOL A:977 , HOH A:1467 , HOH A:1705BINDING SITE FOR RESIDUE GOL A 976
14BC5SOFTWAREASN A:259 , GLY A:261 , LYS A:274 , TYR A:275 , ARG A:783 , GOL A:976 , GOL A:982 , HOH A:1776 , HOH A:1789BINDING SITE FOR RESIDUE GOL A 977
15BC6SOFTWARETHR A:284 , LYS A:286 , LEU A:714 , LYS A:748 , HOH A:874 , GOL A:981 , HOH A:1498 , HOH A:1758BINDING SITE FOR RESIDUE GOL A 978
16BC7SOFTWAREVAL A:162 , GLN A:177 , VAL A:529 , GLN A:549 , GLN A:550 , PHE A:553 , GOL A:983 , HOH A:1040 , HOH A:1469 , HOH A:1575 , HOH A:1777BINDING SITE FOR RESIDUE GOL A 979
17BC8SOFTWARETHR A:284 , LYS A:286 , ASP A:287 , LEU A:714 , LYS A:748 , HOH A:874 , GOL A:978 , HOH A:1498 , HOH A:1758BINDING SITE FOR RESIDUE GOL A 981
18BC9SOFTWARELYS A:274 , TYR A:275 , ARG A:783 , GOL A:971 , GOL A:977BINDING SITE FOR RESIDUE GOL A 982
19CC1SOFTWAREGLN A:177 , VAL A:529 , GLN A:550 , GOL A:979 , HOH A:1226 , HOH A:1469 , HOH A:1777BINDING SITE FOR RESIDUE GOL A 983

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QJX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:121 -Ala A:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QJX)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.AMPN_ECOLI294-303  1A:294-303

(-) Exons   (0, 0)

(no "Exon" information available for 3QJX)

(-) 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:867
 aligned with AMPN_ECOLI | P04825 from UniProtKB/Swiss-Prot  Length:870

    Alignment length:867
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           870 
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864     | 
           AMPN_ECOLI     5 PQAKYRHDYRAPDYQITDIDLTFDLDAQKTVVTAVSQAVRHGASDAPLRLNGEDLKLVSVHINDEPWTAWKEEEGALVISNLPERFTLKIINEISPAANTALEGLYQSGDALCTQCEAEGFRHITYYLDRPDVLARFTTKIIADKIKYPFLLSNGNRVAQGELENGRHWVQWQDPFPKPCYLFALVAGDFDVLRDTFTTRSGREVALELYVDRGNLDRAPWAMTSLKNSMKWDEERFGLEYDLDIYMIVAVDFFNMGAMENKGLNIFNSKYVLARTDTATDKDYLDIERVIGHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSSDLGSRAVNRINNVRTMRGLQFAEDASPMAHPIRPDMVIEMNNFYTLTVYEKGAEVIRMIHTLLGEENFQKGMQLYFERHDGSAATCDDFVQAMEDASNVDLSHFRRWYSQSGTPIVTVKDDYNPETEQYTLTISQRTPATPDQAEKQPLHIPFAIELYDNEGKVIPLQKGGHPVNSVLNVTQAEQTFVFDNVYFQPVPALLCEFSAPVKLEYKWSDQQLTFLMRHARNDFSRWDAAQSLLATYIKLNVARHQQGQPLSLPVHVADAFRAVLLDEKIDPALAAEILTLPSVNEMAELFDIIDPIAIAEVREALTRTLATELADELLAIYNANYQSEYRVEHEDIAKRTLRNACLRFLAFGETHLADVLVSKQFHEANNMTDALAALSAAVAAQLPCRDALMQEYDDKWHQNGLVMDKWFILQATSPAANVLETVRGLLQHRSFTMSNPNRIRSLIGAFAGSNPAAFHAEDGSGYLFLVEMLTDLNSRNPQVASRLIEPLIRLKRYDAKRQEKMRAALEQLKGLENLSGDLYEKITKALA-   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhh....eeeeeeeeeee.....eeeeeeeeeee.......eeee....eeeeeee..ee...eeee..eeee.....eeeeeeeeeehhhhh....eeeee..eeeee....hhhhh..........eeeeeeeeee.....eeee..eeeeeee....eeeeeeeeeeeehhhhh.eeee..eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeee.hhh.......hhhhhhhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhhh......hhhhhh....eeeeeeeee....eeeeeeeee..............eeeeeeee.........ee..ee...eeee...eeeeee.......eeee........eee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qjx A   5 PQAKYRHDYRAPDYQITDIDLTFDLDAQKTVVTAVSQAVRHGASDAPLRLNGEDLKLVSVHINDEPWTAWKEEEGALVISNLPERFTLKIINEISPAANTALEGLYQSGDALCTQCEAEGFRHITYYLDRPDVLARFTTKIIADKIKYPFLLSNGNRVAQGELENGRHWVQWQDPFPKPCYLFALVAGDFDVLRDTFTTRSGREVALELYVDRGNLDRAPWAMTSLKNSMKWDEERFGLEYDLDIYMIVAVDFFNMGAMENKGLNIFNSKYVLARTDTATDKDYLDIERVIGHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSSDLGSRAVNRINNVRTMRGLQFAEDASPMAHPIRPDMVIEMNNFYTLTVYEKGAEVIRMIHTLLGEENFQKGMQLYFERHDGSAATCDDFVQAMEDASNVDLSHFRRWYSQSGTPIVTVKDDYNPETEQYTLTISQRTPATPDQAEKQPLHIPFAIELYDNEGKVIPLQKGGHPVNSVLNVTQAEQTFVFDNVYFQPVPALLCEFSAPVKLEYKWSDQQLTFLMRHARNDFSRWDAAQSLLATYIKLNVARHQQGQPLSLPVHVADAFRAVLLDEKIDPALAAEILTLPSVNEMAELFDIIDPIAIAEVREALTRTLATELADELLAIYNANYQSEYRVEHEDIAKRTLRNACLRFLAFGETHLADVLVSKQFHEANNMTDALAALSAAVAAQLPCRDALMQEYDDKWHQNGLVMDKWFILQATSPAANVLETVRGLLQHRSFTMSNPNRIRSLIGAFAGSNPAAFHAEDGSGYLFLVEMLTDLNSRNPQVASRLIEPLIRLKRYDAKRQEKMRAALEQLKGLENLSGDLYEKITKALAS 900
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           870|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            900
   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  (0, 0)

(no "SCOP Domain" information available for 3QJX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QJX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QJX)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMPN_ECOLI | P04825)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0070006    metalloaminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from 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:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0043171    peptide catabolic process    The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  Cis Peptide Bonds
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  3qjx
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMPN_ECOLI | P04825: 2dq6 2dqm 2hpo 2hpt 2zxg 3b2p 3b2x 3b34 3b37 3b3b 3ked 3puu 4q4e 4q4i 4xmt 4xmu 4xmv 4xmw 4xmx 4xmz 4xn1 4xn2 4xn4 4xn5 4xn7 4xn8 4xn9 4xna 4xnb 4xnd 4xo3 4xo4 4xo5 5mfr 5mfs 5mft

(-) Related Entries Specified in the PDB File

2hpo STRUCTURE OF AMINOPEPTIDASE N FROM E. COLI SUGGESTS A COMPARTMENTALIZED, GATED ACTIVE SITE