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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE X-PROLYL DIPEPTIDYL AMINOPEPTIDASE FROM LACTOCOCCUS LACTIS
 
Authors :  P. Rigolet, I. Mechin, M. M. Delage, J. F. Chich
Date :  03 May 02  (Deposition) - 06 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alpha Beta Hydrolase Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Rigolet, I. Mechin, M. M. Delage, J. F. Chich
The Structural Basis For Catalysis And Specificity Of The X-Prolyl Dipepdidyl Aminopeptidase From Lactococcus Lactis
Structure V. 10 1383 2002
PubMed-ID: 12377124  |  Reference-DOI: 10.1016/S0969-2126(02)00851-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - X-PROLYL DIPEPTIDYL AMINOPETIDASE
    Chains: A
    EC Number: 3.4.14.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTIL1
    Expression System Strain: NCDO 763
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PEPX (ORF2)
    Organism Scientific: LACTOCOCCUS LACTIS
    Organism Taxid: 1358
    Synonym: X-PRO DIPEPTIDYL-PEPTIDASE, XAA-PRO DIPEPTIDYL- PEPTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1LNS)

(-) Sites  (0, 0)

(no "Site" information available for 1LNS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1LNS)

(-) 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:763
 aligned with PEPX_LACLC | P22346 from UniProtKB/Swiss-Prot  Length:763

    Alignment length:763
                                    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       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760   
           PEPX_LACLC     1 MRFNHFSIVDKNFDEQLAELDQLGFRWSVFWDEKKILKDFLIQSPSDMTALQATAELDVIEFLKSSIELDWEIFWNIALQLLDFVPNFDFEIGKAFEYAKNSNLPQIEAEMTTENIISAFYYLLCTRRKTGMILVEHWVSEGLLPLDNHYHFFNDKSLATFDSSLLEREVLWVESPVDSEQRGENDLIKIQIIRPKSTEKLPVVMTASPYHLGINDKANDLALHDMNVELEEKTSHEIHVEQKLPQKLSAKAKELPIVDKAPYRFTHGWTYSLNDYFLTRGFASIYVAGVGTRSSDGFQTSGDYQQIYSMTAVIDWLNGRARAYTSRKKTHEIKASWANGKVAMTGKSYLGTMAYGAATTGVEGLELILAEAGISSWYNYYRENGLVRSPGGFPGEDLDVLAALTYSRNLDGADFLKGNAEYEKRLAEMTAALDRKSGDYNQFWHDRNYLINTDKVKADVLIVHGLQDWNVTPEQAYNFWKALPEGHAKHAFLHRGAHIYMNSWQSIDFSETINAYFVAKLLDRDLNLNLPPVILQENSKDQVWTMMNDFGANTQIKLPLGKTAVSFAQFDNNYDDETFKKYSKDFNVFKKDLFENKANEAVIDLELPSMLTINGPVELELRLKLNDTKGFLSAQILDFGQKKRLEDKVRVKDFKVLDRGRNFMLDDLVELPLVESPYQLVTKGFTNLQNQSLLTVSDLKADEWFTIKFELQPTIYHLEKADKLRVILYSTDFEHTVRDNRKVTYEIDLSQSKLIIPIESVKN 763
               SCOP domains d1lnsa1 A:1-145 X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain                                                                       d1lnsa3 A:146-550 X-Prolyl dipeptidyl aminopeptidase PepX, middle domain                                                                                                                                                                                                                                                                                                                                             d1lnsa2 A:551-763 X-Prolyl dipeptidyl aminopeptidase PepX                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------1lnsA02 A:166-213,A:239-372,A:448-548,A:640-677 ------------1lnsA04      1lnsA02 A:166-213,A:239-372,A:448-548,A:640-677  [code=3.40.50.1820, no name defined]                                                 ---------------------------------------------------------------------------1lnsA02 A:166-213,A:239-372,A:448-548,A:640-677  [code=3.40.50.1820, no name defined]                1lnsA04 A:226-238,A:549-639,A:678-759 Galactose-binding domain-like                        1lnsA02                               1lnsA04 A:226-238,A:549-639,A:678-759 Galactose-binding domain-like               ---- CATH domains
               Pfam domains PepX_N-1lnsA03 A:1-143                                                                                                                         ---------------------------------------Peptidase_S15-1lnsA01 A:183-500                                                                                                                                                                                                                                                                                               --------------------------PepX_C-1lnsA02 A:527-760                                                                                                                                                                                                                  --- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh........hhhhhhhhhhhh...hhhhh......hhhhhhhh....hhhhhhhhhhhhh...........hhhhhhhhh.........hhhhhhhhhhhhhhh......hhhhhhhhh..........ee..ee....hhhhheeeeeeee............eeeeeeee......eeeeeee.......hhhhhhhhh............ee.................................hhhhhhhhh...eeeee...............hhhhhhhhhhhhhhhh....ee.......ee....eeeeeeeeeehhhhhhhhhhhh.....eeeeeee....hhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhh.....eeeeee.............hhhhhhhhhhhhhhh..........eeee.......eeee.......eeeee.......eeeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeee....eeeee..eeeeeeee.....eeeeeeeeeeeeeee....eeeeeeee........eeeee..eeeeeeeeeeeeeee..eee..ee........eeeeee...eeeee....eeeeeee..............eeeee....eeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lns A   1 MRFNHFSIVDKNFDEQLAELDQLGFRWSVFWDEKKILKDFLIQSPSDMTALQATAELDVIEFLKSSIELDWEIFWNIALQLLDFVPNFDFEIGKAFEYAKNSNLPQIEAEMTTENIISAFYYLLCTRRKTGMILVEHWVSEGLLPLDNHYHFFNDKSLATFDSSLLEREVLWVESPVDSEQRGENDLIKIQIIRPKSTEKLPVVMTASPYHLGINDKANDLALHDMNVELEEKTSHEIHVEQKLPQKLSAKAKELPIVDKAPYRFTHGWTYSLNDYFLTRGFASIYVAGVGTRSSDGFQTSGDYQQIYSMTAVIDWLNGRARAYTSRKKTHEIKASWANGKVAMTGKSYLGTMAYGAATTGVEGLELILAEAGISSWYNYYRENGLVRSPGGFPGEDLDVLAALTYSRNLDGADFLKGNAEYEKRLAEMTAALDRKSGDYNQFWHDRNYLINTDKVKADVLIVHGLQDWNVTPEQAYNFWKALPEGHAKHAFLHRGAHIYMNSWQSIDFSETINAYFVAKLLDRDLNLNLPPVILQENSKDQVWTMMNDFGANTQIKLPLGKTAVSFAQFDNNYDDETFKKYSKDFNVFKKDLFENKANEAVIDLELPSMLTINGPVELELRLKLNDTKGFLSAQILDFGQKKRLEDKVRVKDFKVLDRGRNFMLDDLVELPLVESPYQLVTKGFTNLQNQSLLTVSDLKADEWFTIKFELQPTIYHLEKADKLRVILYSTDFEHTVRDNRKVTYEIDLSQSKLIIPIESVKN 763
                                    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       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760
   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  (3, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
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  (3, 3)

Asymmetric Unit
(-)
Clan: AB_hydrolase (347)
(-)
Clan: GBD (153)
(-)
Clan: no clan defined [family: PepX_N] (1)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (PEPX_LACLC | P22346)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    GO:0008239    dipeptidyl-peptidase activity    Catalysis of the hydrolysis of N-terminal dipeptides from 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: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:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of 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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1lns
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