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(-) Description

Title :  CRYSTAL STRUCTURE OF RV3671C PROTEASE, INACTIVE FORM
 
Authors :  T. Biswas, J. Small, O. Vandal, S. Ehrt, O. V. Tsodikov
Date :  10 Oct 09  (Deposition) - 13 Oct 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Serine Protease, Disulfide, Oxidative Stress, Bent Helix, Hydrolase, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Biswas, J. Small, O. Vandal, T. Odaira, H. Deng, S. Ehrt, O. V. Tsodikov
Structural Insight Into Serine Protease Rv3671C That Protects M. Tuberculosis From Oxidative And Acidic Stress.
Structure V. 18 1353 2010
PubMed-ID: 20947023  |  Reference-DOI: 10.1016/J.STR.2010.06.017

(-) Compounds

Molecule 1 - POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE
    Chains: A, B
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PET
    Fragment: UNP RESIDUES 179-397
    Gene: MT3772, RV3671C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: SERINE PROTEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3K6Z)

(-) Sites  (0, 0)

(no "Site" information available for 3K6Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K6Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K6Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K6Z)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.Y3671_MYCTO337-348
 		  2A:337-348
B:337-348
Y3671_MYCTU337-348
 		  2A:337-348
B:337-348

(-) Exons   (0, 0)

(no "Exon" information available for 3K6Z)

(-) 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:198
 aligned with Y3671_MYCTO | P9WHR8 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:205
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381     
          Y3671_MYCTO   182 IPVASPDPALVNNPVVAATEPSVVKIRSLAPRCQKVLEGTGFVISPDRVMTNAHVVAGSNNVTVYAGDKPFEATVVSYDPSVDVAILAVPHLPPPPLVFAAEPAKTGADVVVLGYPGGGNFTATPARIREAIRLSGPDIYGDPEPVTRDVYTIRADVEQGDSGGPLIDLNGQVLGVVFGAAIDDAETGFVLTAGEVAGQLAKIGA 386
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh..eeeeeee-------.eeeeeeee..eeeeehhhhh...eeeee....eeeeeeee......eeeee....................eeeeeehhhhh..eeeeeeeeeeeeee..ee.......eeeeeeeee..hhhhh..eee.....eeeeeeee......eeeeeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6z A 182 IPVASPDPALVNNPVVAATEPSVVKIRSL-------LEGTGFVISPDRVMTNAHVVAGSNNVTVYAGDKPFEATVVSYDPSVDVAILAVPHLPPPPLVFAAEPAKTGADVVVLGYPGGGNFTATPARIREAIRLSGPDIYGDPEPVTRDVYTIRADVEQGDSGGPLIDLNGQVLGVVFGAAIDDAETGFVLTAGEVAGQLAKIGA 386
                                   191       201        |-      |221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381     
                                                      210     218                                                                                                                                                                        


Chain A from PDB  Type:PROTEIN  Length:198
 aligned with Y3671_MYCTU | P9WHR9 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:205
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381     
          Y3671_MYCTU   182 IPVASPDPALVNNPVVAATEPSVVKIRSLAPRCQKVLEGTGFVISPDRVMTNAHVVAGSNNVTVYAGDKPFEATVVSYDPSVDVAILAVPHLPPPPLVFAAEPAKTGADVVVLGYPGGGNFTATPARIREAIRLSGPDIYGDPEPVTRDVYTIRADVEQGDSGGPLIDLNGQVLGVVFGAAIDDAETGFVLTAGEVAGQLAKIGA 386
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh..eeeeeee-------.eeeeeeee..eeeeehhhhh...eeeee....eeeeeeee......eeeee....................eeeeeehhhhh..eeeeeeeeeeeeee..ee.......eeeeeeeee..hhhhh..eee.....eeeeeeee......eeeeeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6z A 182 IPVASPDPALVNNPVVAATEPSVVKIRSL-------LEGTGFVISPDRVMTNAHVVAGSNNVTVYAGDKPFEATVVSYDPSVDVAILAVPHLPPPPLVFAAEPAKTGADVVVLGYPGGGNFTATPARIREAIRLSGPDIYGDPEPVTRDVYTIRADVEQGDSGGPLIDLNGQVLGVVFGAAIDDAETGFVLTAGEVAGQLAKIGA 386
                                   191       201        |-      |221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381     
                                                      210     218                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:197
 aligned with Y3671_MYCTO | P9WHR8 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:205
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381     
          Y3671_MYCTO   182 IPVASPDPALVNNPVVAATEPSVVKIRSLAPRCQKVLEGTGFVISPDRVMTNAHVVAGSNNVTVYAGDKPFEATVVSYDPSVDVAILAVPHLPPPPLVFAAEPAKTGADVVVLGYPGGGNFTATPARIREAIRLSGPDIYGDPEPVTRDVYTIRADVEQGDSGGPLIDLNGQVLGVVFGAAIDDAETGFVLTAGEVAGQLAKIGA 386
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh..eeeeee.------.eeeeeeeee..eeeeehhhhh....eeeee..eeeeeeeee......eeeee....................eeeeeehhhhh..eeeeeeeeeeeeee..ee.......eeeeeeee...hhhhh..eee.....eeeeeeee..--..eeeeeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6z B 182 IPVASPDPALVNNPVVAATEPSVVKIRSL------VLEGTGFVISPDRVMTNAHVVAGSNNVTVYAGDKPFEATVVSYDPSVDVAILAVPHLPPPPLVFAAEPAKTGADVVVLGYPGGGNFTATPARIREAIRLSGPDIYGDPEPVTRDVYTIRADVEQGDSGGPLIDLNGQVLGVVFGAAI--AETGFVLTAGEVAGQLAKIGA 386
                                   191       201        |-     | 221       231       241       251       261       271       281       291       301       311       321       331       341       351       361 |  |  371       381     
                                                      210    217                                                                                                                                               363  |                    
                                                                                                                                                                                                                  366                    


Chain B from PDB  Type:PROTEIN  Length:197
 aligned with Y3671_MYCTU | P9WHR9 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:205
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381     
          Y3671_MYCTU   182 IPVASPDPALVNNPVVAATEPSVVKIRSLAPRCQKVLEGTGFVISPDRVMTNAHVVAGSNNVTVYAGDKPFEATVVSYDPSVDVAILAVPHLPPPPLVFAAEPAKTGADVVVLGYPGGGNFTATPARIREAIRLSGPDIYGDPEPVTRDVYTIRADVEQGDSGGPLIDLNGQVLGVVFGAAIDDAETGFVLTAGEVAGQLAKIGA 386
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh..eeeeee.------.eeeeeeeee..eeeeehhhhh....eeeee..eeeeeeeee......eeeee....................eeeeeehhhhh..eeeeeeeeeeeeee..ee.......eeeeeeee...hhhhh..eee.....eeeeeeee..--..eeeeeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6z B 182 IPVASPDPALVNNPVVAATEPSVVKIRSL------VLEGTGFVISPDRVMTNAHVVAGSNNVTVYAGDKPFEATVVSYDPSVDVAILAVPHLPPPPLVFAAEPAKTGADVVVLGYPGGGNFTATPARIREAIRLSGPDIYGDPEPVTRDVYTIRADVEQGDSGGPLIDLNGQVLGVVFGAAI--AETGFVLTAGEVAGQLAKIGA 386
                                   191       201        |-     | 221       231       241       251       261       271       281       291       301       311       321       331       341       351       361 |  |  371       381     
                                                      210    217                                                                                                                                               363  |                    
                                                                                                                                                                                                                  366
   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 3K6Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K6Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3K6Z)

(-) Gene Ontology  (13, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Y3671_MYCTO | P9WHR8)
molecular function
    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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-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.
    GO:0009403    toxin biosynthetic process    The chemical reactions and pathways resulting in the formation of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A,B   (Y3671_MYCTU | P9WHR9)
molecular function
    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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0001101    response to acid chemical    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form.
    GO:0009403    toxin biosynthetic process    The chemical reactions and pathways resulting in the formation of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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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 Databases and Analysis Tools

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  3k6z
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  Y3671_MYCTO | P9WHR8
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  3.4.21.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        Y3671_MYCTO | P9WHR8: 3k6y 3lt3
        Y3671_MYCTU | P9WHR9: 3k6y 3lt3

(-) Related Entries Specified in the PDB File

3k6y