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(-) Description

Title :  CRYSTAL STRUCTURE OF RV0983 FROM MYCOBACTERIUM TUBERCULOSIS-PROTEOLYTICALLY ACTIVE FORM
 
Authors :  S. K. Palaninathan, N. N. Mohamedmohaideen, J. C. Sacchettini, Tb Str Genomics Consortium (Tbsgc)
Date :  13 Dec 04  (Deposition) - 18 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Serine Protease, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. K. Palaninathan, N. N. Mohamedmohaideen, J. C. Sacchettini
Possible Role For Htra Homologs In Mycobacterium Tuberculosis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN RV0983
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: B121DE3
    Expression System Taxid: 562
    Fragment: SERINE PROTEASE - HTRA
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1Y8T)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y8T)

(-) Cis Peptide Bonds  (13, 13)

Asymmetric/Biological Unit
No.Residues
1Asp A:72 -Gly A:73
2Gly A:224 -Lys A:225
3Lys A:239 -Asp A:240
4Asp A:299 -Pro A:300
5Pro A:300 -Ser A:301
6Gly B:224 -Lys B:225
7Gln B:234 -Val B:235
8Thr B:306 -Val B:307
9Val B:307 -Gln B:308
10Gly C:96 -Val C:97
11Ser C:143 -Thr C:144
12Gln C:151 -Asn C:152
13Gln C:234 -Val C:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y8T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y8T)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y8T)

(-) 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:283
 aligned with O53896_MYCTU | O53896 from UniProtKB/TrEMBL  Length:464

    Alignment length:309
                                   163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453         
         O53896_MYCTU   154 GSVEQVAAKVVPSVVMLETDLGRQSEEGSGIILSAEGLILTNNHVIAAAAKPPLGSPPPKTTVTFSDGRTAPFTVVGADPTSDIAVVRVQGVSGLTPISLGSSSDLRVGQPVLAIGSPLGLEGTVTTGIVSALNRPVSTTGEAGNQNTVLDAIQTDAAINPGNSGGALVNMNAQLVGVNSAIATLGADSADAQSGSIGLGFAIPVDQAKRIADELISTGKASHASLGVQVTNDKDTLGAKIVEVVAGGAAANAGVPKGVVVTKVDDRPINSADALVAAVRSKAPGATVALTFQDPSGGSRTVQVTLGKA 462
               SCOP domains d1y8ta2 A:6-226 Prote    ase PepD                                                                                                                                                                                            d1y8ta1 A:227-314 Protease PepD                                                          SCOP domains
               CATH domains 1y8tA01 A:6-101 Tryps    in-like serine proteases                                               1y8tA02 A:102-226 Trypsin-like serine prote       ases                                                                       ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeeeee.----.eeeeee.....eeeeehhhhh...--------.eeeeee....ee..eeee......eeeee..........ee..........eeeeeehhhhh..eeeeeeeeeeeeee..-------...eeeeee..........eeee....eeeeeeeee...-------.......eeeeehhhhhhhhhhhhh......ee..eeee.......eeeeee...............eeeee..ee..hhhhhhhhhhh.....eeeeeee.....eeeeeee.ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y8t A   6 GSVEQVAAKVVPSVVmLETDL----EEGSGIILSAEGLILTNNHVIAAAA--------PKTTVTFSDGRTAPFTVVGADPTSDIAVVRVQGVSGLTPISLGSSSDLRVGQPVLAIGSPLGLEGTVTTGIVSALNRPVST-------NTVLDAIQTDAAINPGNSGGALVNmNAQLVGVNSAIATL-------QSGSIGLGFAIPVDQAKRIADELISTGKASHASLGVQVTNDKDTLGAKIVEVVAGGAAANAGVPKGVVVTKVDDRPINSADALVAAVRSKAPGATVALTFQDPSGGSRTVQVTLGKA 314
                                    15     |  25|    |  35        45        55        65        75        85        95       105       115       125       135        |-      |155       165       175|      185    |    -  |    205       215       225       235       245       255       265       275       285       295       305         
                                          21-MSE6   31                      55       64                                                                             144     152                     176-MSE       190     198                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:272
 aligned with O53896_MYCTU | O53896 from UniProtKB/TrEMBL  Length:464

    Alignment length:309
                                   163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453         
         O53896_MYCTU   154 GSVEQVAAKVVPSVVMLETDLGRQSEEGSGIILSAEGLILTNNHVIAAAAKPPLGSPPPKTTVTFSDGRTAPFTVVGADPTSDIAVVRVQGVSGLTPISLGSSSDLRVGQPVLAIGSPLGLEGTVTTGIVSALNRPVSTTGEAGNQNTVLDAIQTDAAINPGNSGGALVNMNAQLVGVNSAIATLGADSADAQSGSIGLGFAIPVDQAKRIADELISTGKASHASLGVQVTNDKDTLGAKIVEVVAGGAAANAGVPKGVVVTKVDDRPINSADALVAAVRSKAPGATVALTFQDPSGGSRTVQVTLGKA 462
               SCOP domains d1y8tb2 B:6-226 Prot    ease PepD                                                                                                                                                                                            d1y8tb1 B:227   -314 Protease PepD                                                       SCOP domains
               CATH domains 1y8tB01 B:6-102 Tryp    sin-like serine proteases                                                1y8tB02 B:103-226 Trypsin-like serine prot       eases                                                                      -------------   ------------------------------------------------------         --------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..eeeeee.----.eeeeeee.....eeeehhhhhh..---------..eeee.....ee..eeeeee....eeeee.............hhhhh....eeeeeehhhhh..eeeeeeeeeeeeeee.-------..eeeeeee...........eeee....eeeeeeee....-----........eeeeehhhhhhhhhhhhhh................---.ee.......hhhhhh......ee.ee..ee..hhhhhhhhhhh.....ee.ee---------...ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y8t B   6 GSVEQVAAKVVPSVVmLETD----SEEGSGIILSAEGLILTNNHVIAAA---------PKTTVTFSDGRTAPFTVVGADPTSDIAVVRVQGVSGLTPISLGSSSDLRVGQPVLAIGSPLGLEGTVTTGIVSALNRPVST-------NTVLDAIQTDAAINPGNSGGALVNmNAQLVGVNSAIATLG-----AQSGSIGLGFAIPVDQAKRIADELISTGKASHASLGVQVTNDK---GAKIVEVVAGGAAANAGVPKGVVVTKVDDRPINSADALVAAVRSKAPGATVALT---------TVQVTLGKA 314
                                    15     |  25    |   35        45        |-        65        75        85        95       105       115       125       135        |-      |155       165       175|      185     |   - |     205       215       225       235   |   245       255       265       275       285       295|        -|        
                                          21-MSE   30                      54        64                                                                             144     152                     176-MSE        191   197                                       239 243                                                  296       306        


Chain C from PDB  Type:PROTEIN  Length:255
 aligned with O53896_MYCTU | O53896 from UniProtKB/TrEMBL  Length:464

    Alignment length:309
                                   163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453         
         O53896_MYCTU   154 GSVEQVAAKVVPSVVMLETDLGRQSEEGSGIILSAEGLILTNNHVIAAAAKPPLGSPPPKTTVTFSDGRTAPFTVVGADPTSDIAVVRVQGVSGLTPISLGSSSDLRVGQPVLAIGSPLGLEGTVTTGIVSALNRPVSTTGEAGNQNTVLDAIQTDAAINPGNSGGALVNMNAQLVGVNSAIATLGADSADAQSGSIGLGFAIPVDQAKRIADELISTGKASHASLGVQVTNDKDTLGAKIVEVVAGGAAANAGVPKGVVVTKVDDRPINSADALVAAVRSKAPGATVALTFQDPSGGSRTVQVTLGKA 462
               SCOP domains d1y8tc2 C:6-226 Prot     ease PepD                                                                                                                                                                                           d1y8tc1 C:2    27-314 P   rot    ease PepD                                               SCOP domains
               CATH domains 1y8tC01 C:6-103 Tryp     sin-like serine proteases                                                1y8tC02 C:104-227 Trypsin-like serine pro      teases                                                                       ----------    --------   ---    ----------- --------------------  -                ---- CATH domains
           Pfam domains (1) --------------------     --Trypsin_2-1y8tC04 C:33-18     3                                                                                                                        -------        ------------------------------PDZ_2-1y8    tC01 C:2   29-    311                                                 --- Pfam domains (1)
           Pfam domains (2) --------------------     --Trypsin_2-1y8tC05 C:33-18     3                                                                                                                        -------        ------------------------------PDZ_2-1y8    tC02 C:2   29-    311                                                 --- Pfam domains (2)
           Pfam domains (3) --------------------     --Trypsin_2-1y8tC06 C:33-18     3                                                                                                                        -------        ------------------------------PDZ_2-1y8    tC03 C:2   29-    311                                                 --- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhh..eeeeeee-----.eeeeee.....eeeehhhhhhhhhh.-----..eeeee.....ee.eeeeeee....eeeeee.........ee.hhhhh....eeeeeehhhhh..eeeeeeeeeeeeeee.------...eeeeeee...........eee....eeeeeeeee...--------......eeeeehhhhhhhhhhhhhh.....ee...eee.----...eeee.---...----...........-....hhhhhhhhhh......--.----------------.ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y8t C   6 GSVEQVAAKVVPSVVmLETD-----EEGSGIILSAEGLILTNNHVIAAAAKP-----PPKTTVTFSDGRTAPFTVVGADPTSDIAVVRVQGVSGLTPISLGSSSDLRVGQPVLAIGSPLGLEGTVTTGIVSALNRPVST------QNTVLDAIQTDAAINPGNSGGALVNmNAQLVGVNSAIATL--------SGSIGLGFAIPVDQAKRIADELISTGKASHASLGVQVTN----LGAKIVEV---GAA----VPKGVVVTKVD-RPINSADALVAAVRSKAPGA--A----------------LGKA 314
                                    15     |  25     |  35        45        55 |     |65        75        85        95       105       115       125       135        |-     | 155       165       175|      185    |    -   |   205       215       225       235 |    |245   |   255    |  265    | |275       285     |  |-         -     |   
                                          21-MSE    31                        57    63                                                                              144    151                      176-MSE       190      199                                   237  242    249 253 |  260       270 |                291  |              311   
                                                                                                                                                                                                                                                                                   255              272                   294
   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, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: PDZ-like (184)
(-)
Clan: Peptidase_PA (797)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (O53896_MYCTU | O53896)
molecular function
    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).
    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: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:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006950    response to stress    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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  Cis Peptide Bonds
    Asp A:299 - Pro A:300   [ RasMol ]  
    Asp A:72 - Gly A:73   [ RasMol ]  
    Gln B:234 - Val B:235   [ RasMol ]  
    Gln C:151 - Asn C:152   [ RasMol ]  
    Gln C:234 - Val C:235   [ RasMol ]  
    Gly A:224 - Lys A:225   [ RasMol ]  
    Gly B:224 - Lys B:225   [ RasMol ]  
    Gly C:96 - Val C:97   [ RasMol ]  
    Lys A:239 - Asp A:240   [ RasMol ]  
    Pro A:300 - Ser A:301   [ RasMol ]  
    Ser C:143 - Thr C:144   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        O53896_MYCTU | O53896: 2z9i

(-) Related Entries Specified in the PDB File

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