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(-) Description

Title :  CRYSTAL STRUCTURE OF LEUCYL AMINOPEPTIDASE (PEPA) FROM XOO0834, XANTHOMONAS ORYZAE PV. ORYZAE KACC10331
 
Authors :  S. Natarajan, K. -H. Huynh, L. W. Kang
Date :  08 Sep 09  (Deposition) - 08 Sep 10  (Release) - 08 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Bacterial Blight, Xoo0834, Pepa, Xanthomonas Oryzae Pv. Oryzae Kacc10331, Aminopeptidase, Hydrolase, Manganese, Metal-Binding, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Natarajan, K. -H. Huynh, L. W. Kang
Crystal Structure Of Leucyl Aminopeptidase (Pepa) From Xoo0834, Xanthomonas Oryzae Pv. Oryzae Kacc10331
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE CYTOSOL AMINOPEPTIDASE
    ChainsB, A
    EC Number3.4.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePEPA, XOO0834
    Organism ScientificXANTHOMONAS ORYZAE PV. ORYZAE
    Organism Taxid64187
    StrainKACC10331
    SynonymLEUCINE AMINOPEPTIDASE, LAP, LEUCYL AMINOPEPTIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CO32Ligand/IonCARBONATE ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CO36Ligand/IonCARBONATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:345 , GLU B:346 , GLY B:347 , ARG B:348 , LEU B:372 , HOH B:535BINDING SITE FOR RESIDUE CO3 B 491
2AC2SOFTWARELYS B:262 , ASP B:267 , ASP B:285 , GLU B:346 , ZN B:632BINDING SITE FOR RESIDUE ZN B 631
3AC3SOFTWAREASP B:267 , ASP B:344 , GLU B:346 , HOH B:534 , ZN B:631BINDING SITE FOR RESIDUE ZN B 632
4AC4SOFTWAREASP B:320 , HOH B:573 , HOH B:635BINDING SITE FOR RESIDUE CA B 634
5AC5SOFTWARELYS A:262 , ALA A:345 , GLU A:346 , GLY A:347 , ARG A:348 , LEU A:372BINDING SITE FOR RESIDUE CO3 A 491
6AC6SOFTWAREASP A:267 , ASP A:344 , GLU A:346 , ZN A:630BINDING SITE FOR RESIDUE ZN A 629
7AC7SOFTWARELYS A:262 , ASP A:267 , ASP A:285 , GLU A:346 , ZN A:629BINDING SITE FOR RESIDUE ZN A 630
8AC8SOFTWAREASP A:320 , HOH A:611 , HOH A:615BINDING SITE FOR RESIDUE CA A 633

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg B:476 -Pro B:477
2Arg A:476 -Pro A:477

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOSOL_APPS00631 Cytosol aminopeptidase signature.AMPA_XANOR342-349
 
  2A:342-349
B:342-349
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOSOL_APPS00631 Cytosol aminopeptidase signature.AMPA_XANOR342-349
 
  6A:342-349
B:342-349

(-) Exons   (0, 0)

(no "Exon" information available for 3JRU)

(-) 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:490
 aligned with AMPA_XANOR | Q5H4N2 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:490
                                    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
           AMPA_XANOR     1 MALQFTLNQDAPASAAVDCIVVGAFADKTLSPAAQALDSASQGRLTALLARGDVAGKTGSTTLLHDLPGVAAPRVLVVGLGDAGKFGVAPYLKAIGDATRALKTGAVGTALLTLTELTVKARDAAWNIRQAVTVSDHAAYRYTATLGKKKVDETGLTTLAIAGDDARALAVGVATAEGVEFARELGNLPPNYCTPAYLADTAAAFAGKFPGAEAEILDEAQMEALGMGSLLSVARGSANRPRLIVLKWNGGGDARPYVLVGKGITFDTGGVNLKTQGGIEEMKYDMCGGATVIGTFVATVKAELPINLVVVVPAVENAIDGNAYRPSDVITSMSGKTIEVGNTDAEGRLILCDALTYAERFNPEALVDVATLTGACMVALGHQTAGLMSKHDDLANELLAAGEHVFDRAWRLPLWDEYQGLLDSTFADVYNIGGRWGGAITAGCFLSRFTENQRWAHLDIAGVASDEGKRGMATGRPVGLLTQWLLDRAA 490
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeeee......hhhhhhhhhhh.hhhhhhhhh.........eeeee........eeeeee..hhhhhhhhhhhhhhhhhhhhhh.....eeee.hhhh.....hhhhhhhhhhhhhhhhhh.................eeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh......eeeeeeee.......eeeee.eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee...........eee.....eee......hhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhh...eeeee.hhhhhhhhhhhhhhh...eee...hhhhhhhhh.....ee......hhhhhhhhhhhh......eeeee.................hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOSOL_--------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jru A   1 MALQFTLNQDAPASAAVDCIVVGAFADKTLSPAAQALDSASQGRLTALLARGDVAGKTGSTTLLHDLPGVAAPRVLVVGLGDAGKFGVAPYLKAIGDATRALKTGAVGTALLTLTELTVKARDAAWNIRQAVTVSDHAAYRYTATLGKKKVDETGLTTLAIAGDDARALAVGVATAEGVEFARELGNLPPNYCTPAYLADTAAAFAGKFPGAEAEILDEAQMEALGMGSLLSVARGSANRPRLIVLKWNGGGDARPYVLVGKGITFDTGGVNLKTQGGIEEMKYDMCGGATVIGTFVATVKAELPINLVVVVPAVENAIDGNAYRPSDVITSMSGKTIEVGNTDAEGRLILCDALTYAERFNPEALVDVATLTGACMVALGHQTAGLMSKHDDLANELLAAGEHVFDRAWRLPLWDEYQGLLDSTFADVYNIGGRWGGAITAGCFLSRFTENQRWAHLDIAGVASDEGKRGMATGRPVGLLTQWLLDRAA 490
                                    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

Chain B from PDB  Type:PROTEIN  Length:490
 aligned with AMPA_XANOR | Q5H4N2 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:490
                                    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
           AMPA_XANOR     1 MALQFTLNQDAPASAAVDCIVVGAFADKTLSPAAQALDSASQGRLTALLARGDVAGKTGSTTLLHDLPGVAAPRVLVVGLGDAGKFGVAPYLKAIGDATRALKTGAVGTALLTLTELTVKARDAAWNIRQAVTVSDHAAYRYTATLGKKKVDETGLTTLAIAGDDARALAVGVATAEGVEFARELGNLPPNYCTPAYLADTAAAFAGKFPGAEAEILDEAQMEALGMGSLLSVARGSANRPRLIVLKWNGGGDARPYVLVGKGITFDTGGVNLKTQGGIEEMKYDMCGGATVIGTFVATVKAELPINLVVVVPAVENAIDGNAYRPSDVITSMSGKTIEVGNTDAEGRLILCDALTYAERFNPEALVDVATLTGACMVALGHQTAGLMSKHDDLANELLAAGEHVFDRAWRLPLWDEYQGLLDSTFADVYNIGGRWGGAITAGCFLSRFTENQRWAHLDIAGVASDEGKRGMATGRPVGLLTQWLLDRAA 490
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------Peptidase_M17_N-3jruB01 B:21-150                                                                                                  ----------------------------Peptidase_M17-3jruB03 B:179-483                                                                                                                                                                                                                                                                                  ------- Pfam domains (1)
           Pfam domains (2) --------------------Peptidase_M17_N-3jruB02 B:21-150                                                                                                  ----------------------------Peptidase_M17-3jruB04 B:179-483                                                                                                                                                                                                                                                                                  ------- Pfam domains (2)
         Sec.struct. author ...eeeee..........eeeeee......hhhhhhhhhhh.hhhhhhhhh.........eeeee........eeeeee..hhhhhhhhhhhhhhhhhhhhhh.....eeee.hhhh.....hhhhhhhhhhhhhhhhhh.................eeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....eeeeeehhhhhhhh.hhhhhhhhh......eeeeeeee.......eeeee.eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee...........eee.....eee......hhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhh...eeeee.hhhhhhhhhhhhhhh...eee...hhhhhhhhh.....ee......hhhhhhhhhhhh......eeeee.................hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOSOL_--------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jru B   1 MALQFTLNQDAPASAAVDCIVVGAFADKTLSPAAQALDSASQGRLTALLARGDVAGKTGSTTLLHDLPGVAAPRVLVVGLGDAGKFGVAPYLKAIGDATRALKTGAVGTALLTLTELTVKARDAAWNIRQAVTVSDHAAYRYTATLGKKKVDETGLTTLAIAGDDARALAVGVATAEGVEFARELGNLPPNYCTPAYLADTAAAFAGKFPGAEAEILDEAQMEALGMGSLLSVARGSANRPRLIVLKWNGGGDARPYVLVGKGITFDTGGVNLKTQGGIEEMKYDMCGGATVIGTFVATVKAELPINLVVVVPAVENAIDGNAYRPSDVITSMSGKTIEVGNTDAEGRLILCDALTYAERFNPEALVDVATLTGACMVALGHQTAGLMSKHDDLANELLAAGEHVFDRAWRLPLWDEYQGLLDSTFADVYNIGGRWGGAITAGCFLSRFTENQRWAHLDIAGVASDEGKRGMATGRPVGLLTQWLLDRAA 490
                                    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

   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 3JRU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: MACRO (14)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (AMPA_XANOR | Q5H4N2)
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: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: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.
biological process
    GO:0019538    protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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