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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE PEPTIDASE T
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDASE T
    Chains: A, B
    EC Number: 3.4.11.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PEPT, B1127
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: TRIPEPTIDE AMINOPEPTIDASE, AMINOTRIPEPTIDASE, TRIPEPTIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric/Biological Unit (2, 16)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
2ZN4Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:78 , ASP A:140 , GLU A:173 , GLU A:174 , ASP A:196 , ZN A:420BINDING SITE FOR RESIDUE ZN A 419
02AC2SOFTWAREASP A:140 , GLU A:174 , HIS A:379 , ZN A:419BINDING SITE FOR RESIDUE ZN A 420
03AC3SOFTWAREHIS B:78 , ASP B:140 , GLU B:173 , ASP B:196 , ZN B:420BINDING SITE FOR RESIDUE ZN B 419
04AC4SOFTWAREASP B:140 , GLU B:174 , HIS B:379 , ZN B:419BINDING SITE FOR RESIDUE ZN B 420
05AC5SOFTWAREHIS A:306 , PRO A:307 , PRO A:330 , HIS A:331 , ARG A:407BINDING SITE FOR RESIDUE SO4 A 421
06AC6SOFTWAREGLY A:380 , LYS A:381 , HIS A:382BINDING SITE FOR RESIDUE SO4 A 422
07AC7SOFTWARELYS A:216 , ARG A:272BINDING SITE FOR RESIDUE SO4 A 423
08AC8SOFTWARELYS A:88 , SO4 A:424 , HOH A:435 , LYS B:88 , SO4 B:425BINDING SITE FOR RESIDUE SO4 B 421
09AC9SOFTWARELYS B:216 , ARG B:272BINDING SITE FOR RESIDUE SO4 B 422
10BC1SOFTWARELYS A:88 , SO4 A:425 , LYS B:88 , SO4 B:421BINDING SITE FOR RESIDUE SO4 A 424
11BC2SOFTWAREHIS A:223 , ARG B:280 , TYR B:319 , GLY B:354BINDING SITE FOR RESIDUE SO4 B 423
12BC3SOFTWAREPRO B:330 , HIS B:331 , ARG B:407BINDING SITE FOR RESIDUE SO4 B 424
13BC4SOFTWAREASP A:15 , GLN A:17 , LYS A:88 , HOH A:471 , SO4 B:421BINDING SITE FOR RESIDUE SO4 B 425
14BC5SOFTWARESO4 A:424 , ASP B:15 , HOH B:433BINDING SITE FOR RESIDUE SO4 A 425
15BC6SOFTWAREGLU A:29 , TRP A:32 , HIS A:36BINDING SITE FOR RESIDUE SO4 A 426
16BC7SOFTWARETRP B:32 , HIS B:36BINDING SITE FOR RESIDUE SO4 B 426

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Val A:25 -Pro A:26
2Asp A:140 -Asp A:141
3Val B:25 -Pro B:26
4Asp B:140 -Asp B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARGE_DAPE_CPG2_1PS00758 ArgE / dapE / ACY1 / CPG2 / yscS family signature 1.PEPT_ECOLI73-82
 		  2A:73-82
B:73-82
2ARGE_DAPE_CPG2_2PS00759 ArgE / dapE / ACY1 / CPG2 / yscS family signature 2.PEPT_ECOLI138-176
 		  2A:138-176
B:138-176

(-) Exons   (0, 0)

(no "Exon" information available for 1VIX)

(-) 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:411
 aligned with PEPT_ECOLI | P29745 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:411
                              1                                                                                                                                                                                                                                                                                                                                                                                                                    408 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408 
           PEPT_ECOLI     - --MDKLLERFLNYVSLDTQSKAGVRQVPSTEGQWKLLHLLKEQLEEMGLINVTLSEKGTLMATLPANVPGDIPAIGFISHVDTSPDCSGKNVNPQIVENYRGGDIALGIGDEVLSPVMFPVLHQLLGQTLITTDGKTLLGADDKAGIAEIMTALAVLQQKKIPHGDIRVAFTPDEEVGKGAKHFDVDAFDARWAYTVDGGGVGELEFENFNAASVNIKIVGNNVHPGTAKGVMVNALSLAARIHAEVPADESPEMTEGYEGFYHLASMKGTVERADMHYIIRDFDRKQFEARKRKMMEIAKKVGKGLHPDCYIELVIEDSYYNMREKVVEHPHILDIAQQAMRDCDIEPELKPIRGGTDGAQLSFMGLPCPNLFTGGYNYHGKHEFVTLEGMEKAVQVIVRIAELTAQRK-   -
               SCOP domains d1vixa1 A:-1-207,A:321-409 Peptidase T (tripeptidase), catalytic domain                                                                                                                                          d1vixa2 A:208-320 Peptidase T (tripeptidase)                                                                     d1vixa1 A:-1-207,A:321-409 Peptidase T (tripeptidase), catalytic domain                   SCOP domains
               CATH domains 1vixA01 A:-1-207,A:320-409 Zn peptidases                                                                                                                                                                         1vixA02 A:208-319  [code=3.30.70.360, no name defined]                                                          1vixA01 A:-1-207,A:320-409 Zn peptidases                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh...eeeee.....eeeee..........eeeeee..............eee.......eee....eee....hhhhhhh....eee.......hhhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhh......hhhhhh..eeeee......eee....eeeeeeeeee....hhhhh.....hhhhhhhhhhhhh..............eeeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh......eeeeeeeeee..hhhhhhh.hhhhhhhhhhhhhh....ee......hhhhhhh.......ee...ee.......eeehhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------ARGE_DAPE_-------------------------------------------------------ARGE_DAPE_CPG2_2  PDB: A:138-176       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vix A  -1 MSLDKLLERFLNYVSLDTQSKAGVRQVPSTEGQWKLLHLLKEQLEEMGLINVTLSEKGTLMATLPANVPGDIPAIGFISHVDTSPDCSGKNVNPQIVENYRGGDIALGIGDEVLSPVMFPVLHQLLGQTLITTDGKTLLGADDKAGIAEIMTALAVLQQKKIPHGDIRVAFTPDEEVGKGAKHFDVDAFDARWAYTVDGGGVGELEFENFNAASVNIKIVGNNVHPGTAKGVMVNALSLAARIHAEVPADESPEMTEGYEGFYHLASMKGTVERADMHYIIRDFDRKQFEARKRKMMEIAKKVGKGLHPDCYIELVIEDSYYNMREKVVEHPHILDIAQQAMRDCDIEPELKPIRGGTDGAQLSFMGLPCPNLFTGGYNYHGKHEFVTLEGMEKAVQVIVRIAELTAQRKE 409
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408 


Chain B from PDB  Type:PROTEIN  Length:410
 aligned with PEPT_ECOLI | P29745 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:410
                              1                                                                                                                                                                                                                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408
           PEPT_ECOLI     - --MDKLLERFLNYVSLDTQSKAGVRQVPSTEGQWKLLHLLKEQLEEMGLINVTLSEKGTLMATLPANVPGDIPAIGFISHVDTSPDCSGKNVNPQIVENYRGGDIALGIGDEVLSPVMFPVLHQLLGQTLITTDGKTLLGADDKAGIAEIMTALAVLQQKKIPHGDIRVAFTPDEEVGKGAKHFDVDAFDARWAYTVDGGGVGELEFENFNAASVNIKIVGNNVHPGTAKGVMVNALSLAARIHAEVPADESPEMTEGYEGFYHLASMKGTVERADMHYIIRDFDRKQFEARKRKMMEIAKKVGKGLHPDCYIELVIEDSYYNMREKVVEHPHILDIAQQAMRDCDIEPELKPIRGGTDGAQLSFMGLPCPNLFTGGYNYHGKHEFVTLEGMEKAVQVIVRIAELTAQRK 408
               SCOP domains d1vixb1 B:-1-207,B:321-408 Peptidase T (tripeptidase), catalytic domain                                                                                                                                          d1vixb2 B:208-320 Peptidase T (tripeptidase)                                                                     d1vixb1 B:-1-207,B:321-408 Peptidase T (tripeptidase), catalytic domain                  SCOP domains
               CATH domains 1vixB01 B:-1-207,B:320-408 Zn peptidases                                                                                                                                                                         1vixB02 B:208-319  [code=3.30.70.360, no name defined]                                                          1vixB01 B:-1-207,B:320-408 Zn peptidases                                                  CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------Peptidase_M20-1vixB01 B:74-403                                                                                                                                                                                                                                                                                                            ----- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------Peptidase_M20-1vixB02 B:74-403                                                                                                                                                                                                                                                                                                            ----- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M20_dimer-1vixB03 B:205-308                                                                             ---------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M20_dimer-1vixB04 B:205-308                                                                             ---------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhh.eeeee.....eeeee..........eeeeee..............eee.......ee......ee....hhhhhhh....eee.......hhhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhh......hhhhhh..eeeee......eee....eeeeeeeeee....hhhhh.....hhhhhhhhhhhhh....hhhhh.....eeeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh......eeeeeeeeee..hhhhhhh.hhhhhhhhhhhhhh....ee......hhhhhhhh......ee...ee.......eeehhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------ARGE_DAPE_-------------------------------------------------------ARGE_DAPE_CPG2_2  PDB: B:138-176       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vix B  -1 MSLDKLLERFLNYVSLDTQSKAGVRQVPSTEGQWKLLHLLKEQLEEMGLINVTLSEKGTLMATLPANVPGDIPAIGFISHVDTSPDCSGKNVNPQIVENYRGGDIALGIGDEVLSPVMFPVLHQLLGQTLITTDGKTLLGADDKAGIAEIMTALAVLQQKKIPHGDIRVAFTPDEEVGKGAKHFDVDAFDARWAYTVDGGGVGELEFENFNAASVNIKIVGNNVHPGTAKGVMVNALSLAARIHAEVPADESPEMTEGYEGFYHLASMKGTVERADMHYIIRDFDRKQFEARKRKMMEIAKKVGKGLHPDCYIELVIEDSYYNMREKVVEHPHILDIAQQAMRDCDIEPELKPIRGGTDGAQLSFMGLPCPNLFTGGYNYHGKHEFVTLEGMEKAVQVIVRIAELTAQRK 408
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MH (119)
(-)
Clan: no clan defined [family: M20_dimer] (13)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PEPT_ECOLI | P29745)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
    GO:0045148    tripeptide aminopeptidase activity    Catalysis of the release of the N-terminal residue from a tripeptide.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) 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: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:0006518    peptide metabolic process    The chemical reactions and pathways involving peptides, compounds of two or more 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: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

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