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(-) Description

Title :  CRYSTAL STRUCTURE OF CARBOXYMUCONOLACTONE DECARBOXYLASE FAMILY PROTEIN POSSIBLY INVOLVED IN ANTIOXIDATIVE RESPONSE (TM1620) FROM THERMOTOGA MARITIMA AT 1.56 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  13 May 04  (Deposition) - 08 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Tm1620, Carboxymuconolactone Decarboxylase Family Protein Possibly Involved In Antioxidative Response, Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Joint Center For Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Carboxymuconolactone Decarboxylase Family Protein Possibly Involved In Antioxidative Response (Tm1620) From Thermotoga Maritima At 1. 56 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CARBOXYMUCONOLACTONE DECARBOXYLASE FAMILY PROTEIN
    Chains: A, B, C, D, E, F
    EC Number: 4.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1620
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Other Details: POSSIBLY INVOLVED IN ANTIOXIDATIVE RESPONSE
    Strain: MSB8

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2UNL12Ligand/IonUNKNOWN LIGAND

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:58 , CYS A:59 , ASP A:60 , ASP A:61 , HIS A:98 , HOH A:143 , HOH A:154 , HOH A:197 , HIS E:98 , ARG E:101BINDING SITE FOR RESIDUE UNL A 122
02AC2SOFTWAREHOH A:197 , HIS B:98 , ARG B:101 , ARG E:58 , CYS E:59 , ASP E:60 , ASP E:61 , HIS E:98 , HOH E:145 , HOH E:148 , HOH E:194BINDING SITE FOR RESIDUE UNL E 122
03AC3SOFTWAREHIS A:98 , ARG A:101 , ARG B:58 , CYS B:59 , ASP B:60 , ASP B:61 , HIS B:98 , HOH B:135 , HOH B:171BINDING SITE FOR RESIDUE UNL B 122
04AC4SOFTWAREARG C:58 , CYS C:59 , ASP C:60 , ASP C:61 , HIS C:98 , HOH C:156 , HOH C:179 , HOH D:185 , HIS F:98 , ARG F:101BINDING SITE FOR RESIDUE UNL C 122
05AC5SOFTWAREHIS C:98 , ARG C:101 , ARG D:58 , CYS D:59 , ASP D:60 , ASP D:61 , HIS D:98 , HOH D:145 , HOH D:146 , HOH D:185BINDING SITE FOR RESIDUE UNL D 122
06AC6SOFTWAREHIS D:98 , ARG D:101 , ARG F:58 , CYS F:59 , ASP F:60 , ASP F:61 , HIS F:98 , HOH F:130 , HOH F:173BINDING SITE FOR RESIDUE UNL F 122
07AC7SOFTWARELEU C:57 , ARG C:58 , HOH C:185 , LEU D:57 , ARG D:58BINDING SITE FOR RESIDUE UNL C 123
08AC8SOFTWARESER B:93 , ASP E:32 , TYR E:36 , SER E:54 , CYS E:62 , HIS E:66 , VAL F:90BINDING SITE FOR RESIDUE UNL E 123
09AC9SOFTWARESER A:93 , ASP B:32 , TYR B:36 , HIS B:66 , HOH B:198 , VAL C:90BINDING SITE FOR RESIDUE UNL B 123
10BC1SOFTWAREASP A:32 , TYR A:36 , CYS A:62 , HIS A:66 , SER E:93BINDING SITE FOR RESIDUE UNL A 123
11BC2SOFTWARETYR C:36 , SER C:54 , HIS C:66BINDING SITE FOR RESIDUE UNL C 124
12BC3SOFTWARESER D:93 , ASP F:32 , TYR F:36 , SER F:54 , HIS F:66BINDING SITE FOR RESIDUE UNL F 123
13BC4SOFTWAREVAL A:90 , SER C:93 , ASP D:32 , TYR D:36 , SER D:54 , CYS D:62 , HIS D:66BINDING SITE FOR RESIDUE MPD D 123

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:59 -A:62
2B:59 -B:62
3C:59 -C:62
4D:59 -D:62
5E:59 -E:62
6F:59 -F:62

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VKE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VKE)

(-) 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:117
 aligned with Q9X1V5_THEMA | Q9X1V5 from UniProtKB/TrEMBL  Length:121

    Alignment length:118
                                    13        23        33        43        53        63        73        83        93       103       113        
         Q9X1V5_THEMA     4 KKFVEARRELNEKVLSRGTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKNGETISL 121
               SCOP domains d1vkea_ A: Hyp othetical protein TM1620                                                                                SCOP domains
               CATH domains 1vkeA00 A:4-12 1 AhpD-like                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh-...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1vke A   4 KKFVEARRELNEKV-SRGTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKNGETISL 121
                                    13   | |  23        33        43        53        63        73        83        93       103       113        
                                        17 |                                                                                                      
                                          19                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:101
 aligned with Q9X1V5_THEMA | Q9X1V5 from UniProtKB/TrEMBL  Length:121

    Alignment length:101
                                    30        40        50        60        70        80        90       100       110       120 
         Q9X1V5_THEMA    21 GTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKNGETISL 121
               SCOP domains d1vkeb_ B: Hypothetical protein TM1620                                                                SCOP domains
               CATH domains 1vkeB00 B:21-121 AhpD-like                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1vke B  21 GTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKNGETISL 121
                                    30        40        50        60        70        80        90       100       110       120 


Chain C from PDB  Type:PROTEIN  Length:100
 aligned with Q9X1V5_THEMA | Q9X1V5 from UniProtKB/TrEMBL  Length:121

    Alignment length:100
                                    30        40        50        60        70        80        90       100       110       120
         Q9X1V5_THEMA    21 GTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKNGETIS 120
               SCOP domains d1vkec_ C: Hypothetical protein TM1620                                                               SCOP domains
               CATH domains 1vkeC00 C:21-120 AhpD-like                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1vke C  21 GTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKNGETIS 120
                                    30        40        50        60        70        80        90       100       110       120


Chain D from PDB  Type:PROTEIN  Length:101
 aligned with Q9X1V5_THEMA | Q9X1V5 from UniProtKB/TrEMBL  Length:121

    Alignment length:101
                                    28        38        48        58        68        78        88        98       108       118 
         Q9X1V5_THEMA    19 SRGTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKNGETI 119
               SCOP domains d1vked_ D: Hypothetical protein TM1620                                                                SCOP domains
               CATH domains 1vkeD00 D:19-119 AhpD-like                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1vke D  19 SRGTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKNGETI 119
                                    28        38        48        58        68        78        88        98       108       118 


Chain E from PDB  Type:PROTEIN  Length:119
 aligned with Q9X1V5_THEMA | Q9X1V5 from UniProtKB/TrEMBL  Length:121

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
         Q9X1V5_THEMA     2 EYKKFVEARRELNEKVLSRGTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKNGETISL 121
               SCOP domains d1vkee_ E: Hypot hetical protein TM1620                                                                                  SCOP domains
               CATH domains 1vkeE00 E:2-121  AhpD-like                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh-hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vke E   2 EYKKFVEARRELNEKV-SRGTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKNGETISL 121
                                    11     | |21        31        41        51        61        71        81        91       101       111       121
                                          17 |                                                                                                      
                                            19                                                                                                      


Chain F from PDB  Type:PROTEIN  Length:97
 aligned with Q9X1V5_THEMA | Q9X1V5 from UniProtKB/TrEMBL  Length:121

    Alignment length:97
                                    29        39        49        59        69        79        89        99       109       
         Q9X1V5_THEMA    20 RGTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKNG 116
               SCOP domains d1vkef_ F: Hypothetical protein TM1620                                                            SCOP domains
               CATH domains 1vkeF00 F:20-116 AhpD-like                                                                        CATH domains
           Pfam domains (1) ---CMD-1vkeF01 F:23-108                                                                  -------- Pfam domains (1)
           Pfam domains (2) ---CMD-1vkeF02 F:23-108                                                                  -------- Pfam domains (2)
           Pfam domains (3) ---CMD-1vkeF03 F:23-108                                                                  -------- Pfam domains (3)
           Pfam domains (4) ---CMD-1vkeF04 F:23-108                                                                  -------- Pfam domains (4)
           Pfam domains (5) ---CMD-1vkeF05 F:23-108                                                                  -------- Pfam domains (5)
           Pfam domains (6) ---CMD-1vkeF06 F:23-108                                                                  -------- Pfam domains (6)
         Sec.struct. author ..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 1vke F  20 RGTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQEGASDEEIFEALDIALVVGGSIVIPHLRRAVGFLEELREMEKNG 116
                                    29        39        49        59        69        79        89        99       109
   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  (1, 6)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: AhpD-like (9)
(-)
Family: CMD (9)
(-)
Thermotoga maritima (2)
1aCMD-1vkeF01F:23-108
1bCMD-1vkeF02F:23-108
1cCMD-1vkeF03F:23-108
1dCMD-1vkeF04F:23-108
1eCMD-1vkeF05F:23-108
1fCMD-1vkeF06F:23-108

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q9X1V5_THEMA | Q9X1V5)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0051920    peroxiredoxin activity    Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9X1V5_THEMA | Q9X1V5: 1p8c

(-) Related Entries Specified in the PDB File

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