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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FIRST GLUTAREDOXIN DOMAIN OF HUMAN GLUTAREDOXIN 3 (GLRX3)
 
Authors :  M. Vollmar, C. Johansson, R. Cocking, T. Krojer, J. R. C. Muniz, K. L. Kav F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, U. Oppermann
Date :  29 Aug 11  (Deposition) - 29 Feb 12  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Vollmar, C. Johansson, R. Cocking, T. Krojer, J. R. C. Muniz, K. L. Kavanagh, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt A. Edwards, U. Oppermann
Crystal Structure Of The First Glutaredoxin Domain Of Human Glutaredoxin 3 (Glrx3)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTAREDOXIN-3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-CTHF
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    FragmentGLUTAREDOXIN DOMAIN, RESIDUES 130-232
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPKC-INTERACTING COUSIN OF THIOREDOXIN, PICOT, PKC-THETA-INTERACTING PROTEIN, PKCQ-INTERACTING PROTEIN, THIOREDOXIN-LIKE PROTEIN 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:208 , LEU A:209 , ILE A:210 , HOH A:2151 , LEU B:236 , PHE B:238 , GLN B:239BINDING SITE FOR RESIDUE EDO A1240
2AC2SOFTWARETHR A:141 , HIS A:142 , TYR A:194 , GLY A:207 , HOH A:2130BINDING SITE FOR RESIDUE EDO A1241
3AC3SOFTWAREPRO B:154 , HIS B:170 , PHE B:176 , EDO B:1242 , HOH B:2069 , HOH B:2077 , HOH B:2085 , HOH B:2204BINDING SITE FOR RESIDUE EDO B1240
4AC4SOFTWARELYS B:139 , LEU B:140 , ALA B:143 , HOH B:2021 , HOH B:2089BINDING SITE FOR RESIDUE EDO B1241
5AC5SOFTWAREGLN B:155 , EDO B:1240 , HOH B:2037 , HOH B:2042 , HOH B:2204BINDING SITE FOR RESIDUE EDO B1242

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:200 -Pro A:201
2Tyr B:200 -Pro B:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAREDOXIN_2PS51354 Glutaredoxin domain profile.GLRX3_HUMAN134-236
 
236-335
 
  4A:134-232
B:134-232
A:233-238
B:233-238
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAREDOXIN_2PS51354 Glutaredoxin domain profile.GLRX3_HUMAN134-236
 
236-335
 
  2A:134-232
-
A:233-238
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAREDOXIN_2PS51354 Glutaredoxin domain profile.GLRX3_HUMAN134-236
 
236-335
 
  2-
B:134-232
-
B:233-238

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003686441ENSE00002174390chr10:131934663-131934776114GLRX3_HUMAN1-31310--
1.2ENST000003686442ENSE00000728668chr10:131943475-131943583109GLRX3_HUMAN31-67370--
1.4ENST000003686444ENSE00000728671chr10:131958259-13195833375GLRX3_HUMAN68-92250--
1.5bENST000003686445bENSE00000728676chr10:131959060-131959261202GLRX3_HUMAN93-160682A:132-160
B:0-160
29
32
1.6ENST000003686446ENSE00000728678chr10:131964771-131964943173GLRX3_HUMAN160-217582A:160-217
B:160-217
58
58
1.7ENST000003686447ENSE00000728681chr10:131965183-13196524462GLRX3_HUMAN218-238212A:218-232
B:218-232
15
15
1.8ENST000003686448ENSE00000728683chr10:131967697-13196775458GLRX3_HUMAN238-257202A:233-239
B:233-239
7
7
1.9ENST000003686449ENSE00000728687chr10:131969848-13196990053GLRX3_HUMAN258-275180--
1.10ENST0000036864410ENSE00000728691chr10:131973131-13197317040GLRX3_HUMAN275-288140--
1.11ENST0000036864411ENSE00000577957chr10:131973261-13197335393GLRX3_HUMAN289-319310--
1.12aENST0000036864412aENSE00001217321chr10:131977606-13197768479GLRX3_HUMAN320-335160--
1.13bENST0000036864413bENSE00001217252chr10:131978377-131978640264GLRX3_HUMAN-00--

(-) Sequences/Alignments

Asymmetric 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:108
 aligned with GLRX3_HUMAN | O76003 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:121
                                   141       151       161       171       181       191       201       211       221       231       241       251 
          GLRX3_HUMAN   132 DLNLRLKKLTHAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKAYSSWPTYPQLYVSGELIGGLDIIKELEASEELDTICPKAPKLEERLKVLTNKASVMLFM 252
               SCOP domains d3zywa_ A: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...eeeee........hhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhh.hhhhhh...-------------....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --GLUTAREDOXIN_2  PDB: A:134-232 UniProt: 134-236                                                        ---------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------GLUTAREDOXIN_2    PROSITE (2)
           Transcript 1 (1) Exon 1.5b  PDB: A:132-160    ---------------------------------------------------------Exon 1.7 [INCOMPLETE]-------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.6  PDB: A:160-217 UniProt: 160-217                 --------------------Exon 1.8        Transcript 1 (2)
                 3zyw A 132 DLNLRLKKLTHAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKAYSSWPTYPQLYVSGELIGGLDIIKELEASEELDTICPKA-------------AENLYFQ 239
                                   141       151       161       171       181       191       201       211       221       231|        -    |  238 
                                                                                                                              232           233      

Chain B from PDB  Type:PROTEIN  Length:111
 aligned with GLRX3_HUMAN | O76003 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:124
                                   138       148       158       168       178       188       198       208       218       228       238       248    
          GLRX3_HUMAN   129 LKEDLNLRLKKLTHAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKAYSSWPTYPQLYVSGELIGGLDIIKELEASEELDTICPKAPKLEERLKVLTNKASVMLFM 252
               SCOP domains d3zywb_ B: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eeeee........hhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhh.hhhhhh...-------------....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----GLUTAREDOXIN_2  PDB: B:134-232 UniProt: 134-236                                                        ---------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------GLUTAREDOXIN_2    PROSITE (2)
           Transcript 1 (1) Exon 1.5b  PDB: B:0-160         ---------------------------------------------------------Exon 1.7 [INCOMPLETE]-------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.6  PDB: B:160-217 UniProt: 160-217                 --------------------Exon 1.8        Transcript 1 (2)
                 3zyw B   0 MKEDLNLRLKKLTHAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKAYSSWPTYPQLYVSGELIGGLDIIKELEASEELDTICPKA-------------AENLYFQ 239
                            ||     138       148       158       168       178       188       198       208       218       228   |     -       235    
                            0|                                                                                                   232           233      
                           130                                                                                                                          

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GLRX3_HUMAN | O76003)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
    GO:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0010614    negative regulation of cardiac muscle hypertrophy    Any process that decreases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
    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.
    GO:0002026    regulation of the force of heart contraction    Any process that modulates the extent of heart contraction, changing the force with which blood is propelled.
cellular component
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLRX3_HUMAN | O760032diy 2wz9 2yan

(-) Related Entries Specified in the PDB File

2wz9 CRYSTAL STRUCTURE OF THE THIOREDOXIN DOMAIN OF HUMAN TXNL2
2yan CRYSTAL STRUCTURE OF THE SECOND GLUTAREDOXIN DOMAIN OF HUMAN TXNL2