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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
Date :  20 Sep 07  (Deposition) - 10 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I
Keywords :  Serine Protease, Htra, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. N. Mohamedmohaideen, S. K. Palaninathan, P. M. Morin, B. J. Williams, M. Braunstein, S. E. Tichy, J. Locker, D. H. Russell, W. R. Jacobs, J. C. Sacchettini
Structure And Function Of The Virulence-Associated High-Temperature Requirement A Of Mycobacterium Tuberculosis
Biochemistry V. 47 6092 2008
PubMed-ID: 18479146  |  Reference-DOI: 10.1021/BI701929M
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE SERINE PROTEASE PEPD
    ChainsA, B, C
    EC Number3.4.21.-
    FragmentRESIDUES IN DATABASE 149-464
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    SynonymSERINE PROTEINASE, MTB32B
 
Molecule 2 - SVEQV
    ChainsD, E, F
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    Other DetailsAUTOLYTIC PRODUCTS
 
Molecule 3 - GATV
    ChainsG, H, I
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    Other DetailsAUTOLYTIC PRODUCTS

 Structural Features

(-) Chains, Units

  123456789
Asymmetric/Biological Unit ABCDEFGHI

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 2Z9I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z9I)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser C:143 -Thr C:144
2Gln C:151 -Asn C:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z9I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z9I)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z9I)

(-) 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:284
 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 d2z9ia2 A:6-226 Prote    ase PepD                                                                                                                                                                                            d2z9ia1 A:227 -314 Protease PepD                                                         SCOP domains
               CATH domains 2z9iA01 A:6-101 Tryps    in-like serine proteases                                               2z9iA02 A:102-226 Trypsin-like serine prote       ases                                                                       ------------- -------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeeeee.----.eeeeee.....eeeehhhhhhhhhh------..eeeeee....ee..eeeeee....eeeee..........ee.hhhhh....eeeeeehhhhh..eeeeeeeeeeeeeee.-------..eeeeeee..........eeee....eeeeeeeee...-------.......eeeeehhhhhhhhhhhhhhh....ee..eeee...-...eeeeee.....hhhhh.....eeeee..ee..hhhhhhhhhhh.....eeeeeeee...eeeeeeee.ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z9i A   6 GSVEQVAAKVVPSVVmLETDL----EEGSGIILSAEGLILTNNHVIAAAAK------PPKTTVTFSDGRTAPFTVVGADPTSDIAVVRVQGVSGLTPISLGSSSDLRVGQPVLAIGSPLGLEGTVTTGIVSALNRPVST-------NTVLDAIQTDAAINPGNSGGALVNmNAQLVGVNSAIATL-------QSGSIGLGFAIPVDQAKRIADELISTGKASHASLGVQVTNDK-TLGAKIVEVVAGGAAANAGVPKGVVVTKVDDRPINSADALVAAVRSKAPGATVALTFQDPSGGSRTVQVTLGKA 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                       56     63                                                                              144     152                     176-MSE       190     198                                      239 |                                                                         
                                                                                                                                                                                                                                                                     241                                                                         

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with O53896_MYCTU | O53896 from UniProtKB/TrEMBL  Length:464

    Alignment length:312
                                   161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461  
         O53896_MYCTU   152 PPGSVEQVAAKVVPSVVMLETDLGRQSEEGSGIILSAEGLILTNNHVIAAAAKPPLGSPPPKTTVTFSDGRTAPFTVVGADPTSDIAVVRVQGVSGLTPISLGSSSDLRVGQPVLAIGSPLGLEGTVTTGIVSALNRPVSTTGEAGNQNTVLDAIQTDAAINPGNSGGALVNMNAQLVGVNSAIATLGADSADAQSGSIGLGFAIPVDQAKRIADELISTGKASHASLGVQVTNDKDTLGAKIVEVVAGGAAANAGVPKGVVVTKVDDRPINSADALVAAVRSKAPGATVALTFQDPSGGSRTVQVTLGKAE 463
               SCOP domains d2z9ib2 B:4-226 Protea    se PepD                                                                                                                                                                                              d2z9ib1 B:22    7-315 Pr   otease PepD                                                    SCOP domains
               CATH domains 2z9iB01 B:4-101 Trypsi    n-like serine proteases                                                 2z9iB02 B:102-226 Trypsin-like serine prote       ases                                                                       ------------    --------   -------------------------------------------          --------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..eeeeeee----.eeeeeee.....eeeehhhhhh...--------.eeeee.....ee..eeeeee....eeeee..........ee.hhhhh....eeeeeehhhhh..eeeeeeeeeeeeeee.-------..eeeeeee...........eeee...eeeeeeeee...-------.......eeeeehhhhhhhhhhhhhhh....ee........----.ee.....---hhhhhh.....ee.ee..ee..hhhhhhhhhhh.....eee..----------.eee.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z9i B   4 PPGSVEQVAAKVVPSVVmLETD----SEEGSGIILSAEGLILTNNHVIAAAA--------PKTTVTFSDGRTAPFTVVGADPTSDIAVVRVQGVSGLTPISLGSSSDLRVGQPVLAIGSPLGLEGTVTTGIVSALNRPVST-------NTVLDAIQTDAAINPGNSGGALVNmNAQLVGVNSAIATL-------QSGSIGLGFAIPVDQAKRIADELISTGKASHASLGVQVTND----GAKIVEVV---AAANAGVPKGVVVTKVDDRPINSADALVAAVRSKAPGATVALT----------VQVTLGKAE 315
                                    13       |23 |    | 33        43        53 |       -|       73        83        93       103       113       123       133       143|      153       163       173  |    183      |  -    |  203       213       223       233    |  243      |  -|      263       273       283       293  |      -   |   313  
                                            21-MSE   30                       55       64                                                                             144     152                     176-MSE       190     198                                     238  243    250 254                                       296        307        

Chain C from PDB  Type:PROTEIN  Length:260
 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 d2z9ic2 C:6-226 Prot    ease PepD                                                                                                                                                                                            d2z9ic1 C:2    27-314 P   rot    ease PepD                                               SCOP domains
               CATH domains 2z9iC01 C:6-102 Tryp    sin-like serine proteases                                                2z9iC02 C:103-226 Trypsin-like serine prot      eases                                                                       -----------    --------   ---    ----------- ---------------------                  ---- CATH domains
           Pfam domains (1) --------------------    ---Trypsin_2-2z9iC04 C:33-183                                                                                                                             -------        ------------------------------PDZ_2-2z9    iC01 C:2   29-    311                                                 --- Pfam domains (1)
           Pfam domains (2) --------------------    ---Trypsin_2-2z9iC05 C:33-183                                                                                                                             -------        ------------------------------PDZ_2-2z9    iC02 C:2   29-    311                                                 --- Pfam domains (2)
           Pfam domains (3) --------------------    ---Trypsin_2-2z9iC06 C:33-183                                                                                                                             -------        ------------------------------PDZ_2-2z9    iC03 C:2   29-    311                                                 --- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhh..eeeeeee----.eeeeeeeee...eeeehhhhhhhhhh....-...eeeee.....ee.eeeeeee....eeeeee.........ee.hhhhh....eeeeeehhhhh..eeeeeeeeeeeeee..------....eeeeee..........eeee....eeeeeeeee...--------......eeeeehhhhhhhhhhhhhh.....ee...eee.----..eeeee.---...----.....ee....-....hhhhhhhhhhh......------------------.ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z9i C   6 GSVEQVAAKVVPSVVmLETD----SEEGSGIILSAEGLILTNNHVIAAAAKPPLG-PPPKTTVTFSDGRTAPFTVVGADPTSDIAVVRVQGVSGLTPISLGSSSDLRVGQPVLAIGSPLGLEGTVTTGIVSALNRPVST------QNTVLDAIQTDAAINPGNSGGALVNmNAQLVGVNSAIATL--------SGSIGLGFAIPVDQAKRIADELISTGKASHASLGVQVTN----LGAKIVEV---GAA----VPKGVVVTKVD-RPINSADALVAAVRSKAPGAT------------------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   30                            60 |                                                                               144    151                      176-MSE       190      199                                   237  242    249 253 |  260       270 |                 292                311   
                                                                                   62                                                                                                                                                                                              255              272                                          

Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .ee. Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2z9i D 408 VEQV 411

Chain E from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .ee. Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2z9i E 408 VEQV 411

Chain F from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 2z9i F 407 SVEQV 411

Chain G from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .eee Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2z9i G   1 GATV   4

Chain H from PDB  Type:PROTEIN  Length:2
                                  
               SCOP domains -- SCOP domains
               CATH domains -- CATH domains
               Pfam domains -- Pfam domains
         Sec.struct. author .. Sec.struct. author
                 SAPs(SNPs) -- SAPs(SNPs)
                    PROSITE -- PROSITE
                 Transcript -- Transcript
                 2z9i H   3 TV   4

Chain I from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 2z9i I   2 ATV   4

   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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (2, 6)

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

(-) 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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 Related Entries

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

UniProtKB/TrEMBL
        O53896_MYCTU | O538961y8t

(-) Related Entries Specified in the PDB File

1ky9 HTRA PROTEIN
1l1j HTRA PROTEIN
1sot HTRA PROTEIN