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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOPEPTIDASE PEPT (NP_980509.1) FROM BACILLUS CEREUS ATCC 10987 AT 2.04 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  18 Feb 09  (Deposition) - 03 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Np_980509. 1, Aminopeptidase Pept, Peptidase Family M20/M25/M40, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Aminopeptidase, Hydrolase, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Aminopeptidase Pept (Np_980509. 1) From Bacillus Cereus Atcc 10987 At 2. 04 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDASE T
    Atcc: 10987
    Chains: A
    EC Number: 3.4.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BCE_4216, NP_980509.1, PEPT
    Organism Scientific: BACILLUS CEREUS ATCC 10987
    Organism Taxid: 222523

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE10Mod. Amino AcidSELENOMETHIONINE
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 34)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2MSE20Mod. Amino AcidSELENOMETHIONINE
3PEG6Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:179 , HIS A:192 , ASN A:237 , ARG A:250 , TYR A:287 , GLY A:321 , HOH A:438BINDING SITE FOR RESIDUE GOL A 373
2AC2SOFTWARETHR A:36 , VAL A:40 , VAL A:42 , PHE A:292 , ALA A:328 , ILE A:332 , PRO A:333 , GOL A:375 , HOH A:446BINDING SITE FOR RESIDUE GOL A 374
3AC3SOFTWAREGLY A:39 , ASN A:254 , GLY A:289 , GOL A:374 , HOH A:396 , HOH A:440 , HOH A:460 , HOH A:533BINDING SITE FOR RESIDUE GOL A 375
4AC4SOFTWAREASP A:18 , SER A:19 , GLU A:20 , PHE A:23 , ASN A:85BINDING SITE FOR RESIDUE GOL A 376
5AC5SOFTWAREGLY A:194 , VAL A:195 , GLN A:317 , SER A:318BINDING SITE FOR RESIDUE PEG A 377
6AC6SOFTWAREASP A:37 , ARG A:152 , HIS A:330 , HOH A:471BINDING SITE FOR RESIDUE PEG A 378
7AC7SOFTWARELYS A:92 , TYR A:95 , LYS A:350BINDING SITE FOR RESIDUE PEG A 379

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GB0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:82 -Pro A:83
2Asp A:107 -Asp A:108

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GB0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GB0)

(-) Exons   (0, 0)

(no "Exon" information available for 3GB0)

(-) 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:373
 aligned with Q731F0_BACC1 | Q731F0 from UniProtKB/TrEMBL  Length:372

    Alignment length:373
                             1                                                                                                                                                                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369   
         Q731F0_BACC1     - -MINQERLVNEFMELVQVDSETKFEAEICKVLTKKFTDLGVEVFEDDTMAVTGHGAGNLICTLPATKDGVDTIYFTSHMDTVVPGNGIKPSIKDGYIVSDGTTILGADDKAGLASMFEAIRVLKEKNIPHGTIEFIITVGEESGLVGAKALDRERITAKYGYALDSDGKVGEIVVAAPTQAKVNAIIRGKTAHAGVAPEKGVSAITIAAKAIAKMPLGRIDSETTANIGRFEGGTQTNIVCDHVQIFAEARSLINEKMEAQVAKMKEAFETTAKEMGGHADVEVNVMYPGFKFADGDHVVEVAKRAAEKIGRTPSLHQSGGGSDANVIAGHGIPTVNLAVGYEEIHTTNEKIPVEELAKTAELVVAIIEEVAK 372
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..eeee..hhhhhh.....eeeee.........eeeeee............eee..eee.......hhhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh...eeeeeee.....eeeeee.eeeeeeeeee........hhhhh.hhhhhhhhhhh....eeee..eeeeeeeeee.........eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..ee....hhhhhhhhhhhhhh....eeee....hhhhhhhhh...eeeee...........eeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gb0 A   0 GmINQERLVNEFmELVQVDSETKFEAEICKVLTKKFTDLGVEVFEDDTmAVTGHGAGNLICTLPATKDGVDTIYFTSHmDTVVPGNGIKPSIKDGYIVSDGTTILGADDKAGLASmFEAIRVLKEKNIPHGTIEFIITVGEESGLVGAKALDRERITAKYGYALDSDGKVGEIVVAAPTQAKVNAIIRGKTAHAGVAPEKGVSAITIAAKAIAKmPLGRIDSETTANIGRFEGGTQTNIVCDHVQIFAEARSLINEKmEAQVAKmKEAFETTAKEmGGHADVEVNVmYPGFKFADGDHVVEVAKRAAEKIGRTPSLHQSGGGSDANVIAGHGIPTVNLAVGYEEIHTTNEKIPVEELAKTAELVVAIIEEVAK 372
                             |       9  |     19        29        39        49        59        69        79        89        99       109     | 119       129       139       149       159       169       179       189       199       209    |  219       229       239       249       259    |  269     | 279      |289       299       309       319       329       339       349       359       369   
                             |         12-MSE                              48-MSE                        78-MSE                              115-MSE                                                                                            214-MSE                                    257-MSE  |        275-MSE    286-MSE                                                                                  
                             1-MSE                                                                                                                                                                                                                                                                264-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3GB0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GB0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GB0)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q731F0_BACC1 | Q731F0)
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: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.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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