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(-) Description

Title :  CRYSTAL STRUCTURE OF TN501 MERA
 
Authors :  A. Dong, R. Ledwidge, B. Patel, D. Fiedler, M. Falkowski, J. Zelikova, A. O. Summers, E. F. Pai, S. M. Miller
Date :  02 May 05  (Deposition) - 05 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Mercuric Ion Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Ledwidge, B. Patel, A. Dong, D. Fiedler, M. Falkowski, J. Zelikova, A. O. Summers, E. F. Pai, S. M. Miller
Nmera, The Metal Binding Domain Of Mercuric Ion Reductase, Removes Hg(2+) From Proteins, Delivers It To The Catalytic Core, And Protects Cells Under Glutathione-Depleted Conditions
Biochemistry V. 44 11402 2005
PubMed-ID: 16114877  |  Reference-DOI: 10.1021/BI050519D

(-) Compounds

Molecule 1 - MERCURIC REDUCTASE
    Chains: A
    EC Number: 1.16.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET, PJOE114
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MERA
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: HGII, REDUCTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL3Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL6Ligand/IonGLYCEROL
3SO46Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:322 , ARG A:326 , LYS A:449 , GLN A:453 , GOL A:3003 , HOH A:4033 , HOH A:4206 , HOH A:4310BINDING SITE FOR RESIDUE SO4 A 2001
2AC2SOFTWAREARG A:35 , ASN A:272 , THR A:273 , ARG A:274 , SER A:275 , HOH A:4057 , HOH A:4357 , HOH A:4495BINDING SITE FOR RESIDUE SO4 A 2002
3AC3SOFTWARETRP A:164 , SER A:172 , LYS A:262 , HOH A:4036 , HOH A:4248 , HOH A:4360 , HOH A:4364 , HOH A:4390BINDING SITE FOR RESIDUE SO4 A 2003
4AC4SOFTWAREILE A:10 , GLY A:11 , GLY A:13 , GLY A:14 , ALA A:15 , ILE A:33 , GLU A:34 , ARG A:35 , GLY A:40 , THR A:41 , CYS A:42 , GLY A:46 , CYS A:47 , LYS A:51 , GLY A:115 , GLU A:116 , ALA A:117 , ALA A:145 , THR A:146 , GLY A:147 , ARG A:269 , LEU A:276 , GLY A:308 , ASP A:309 , GLN A:315 , PHE A:316 , VAL A:317 , TYR A:318 , PHE A:348 , HOH A:4000 , HOH A:4001 , HOH A:4004 , HOH A:4008 , HOH A:4010 , HOH A:4011 , HOH A:4044 , HOH A:4057 , HOH A:4254 , HOH A:4351BINDING SITE FOR RESIDUE FAD A 666
5AC5SOFTWAREGLN A:6 , GLN A:29 , THR A:31 , THR A:111 , ARG A:135 , HOH A:4026BINDING SITE FOR RESIDUE GOL A 3001
6AC6SOFTWARESER A:161 , TYR A:163 , THR A:165 , GLU A:168 , HOH A:4165 , HOH A:4406BINDING SITE FOR RESIDUE GOL A 3002
7AC7SOFTWAREALA A:321 , THR A:325 , GLN A:453 , SER A:463 , CYS A:464 , CYS A:465 , ALA A:466 , GLY A:467 , SO4 A:2001 , HOH A:4185 , HOH A:4407BINDING SITE FOR RESIDUE GOL A 3003

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:42 -A:47
2A:464 -A:465

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp A:350 -Pro A:351

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZK7)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PYRIDINE_REDOX_1PS00076 Pyridine nucleotide-disulphide oxidoreductases class-I active site.MERA_PSEAI133-143  1A:39-49
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PYRIDINE_REDOX_1PS00076 Pyridine nucleotide-disulphide oxidoreductases class-I active site.MERA_PSEAI133-143  2A:39-49

(-) Exons   (0, 0)

(no "Exon" information available for 1ZK7)

(-) 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:467
 aligned with MERA_PSEAI | P00392 from UniProtKB/Swiss-Prot  Length:561

    Alignment length:467
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       
           MERA_PSEAI    95 NEPPVQVAVIGSGGAAMAAALKAVEQGAQVTLIERGTIGGTCVNVGCVPSKIMIRAAHIAHLRRESPFDGGIAATVPTIDRSKLLAQQQARVDELRHAKYEGILGGNPAITVVHGEARFKDDQSLTVRLNEGGERVVMFDRCLVATGASPAVPPIPGLKESPYWTSTEALASDTIPERLAVIGSSVVALELAQAFARLGSKVTVLARNTLFFREDPAIGEAVTAAFRAEGIEVLEHTQASQVAHMDGEFVLTTTHGELRADKLLVATGRTPNTRSLALDAAGVTVNAQGAIVIDQGMRTSNPNIYAAGDCTDQPQFVYVAAAAGTRAAINMTGGDAALDLTAMPAVVFTDPQVATVGYSEAEAHHDGIETDSRTLTLDNVPRALANFDTRGFIKLVIEEGSHRLIGVQAVAPEAGELIQTAALAIRNRMTVQELADQLFPYLTMVEGLKLAAQTFNKDVKQLSCCAG 561
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeee..eeeeee....eeeee..eeee...eee..............hhhhhhhh.....eeeee..hhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhh..eee....eeeeeee..eeeeee..eeeee.eeee...eee.....hhhhhh.....................eee.........hhhhhhhhhhhhhhhhh...........eeee....eeeeee.hhhhhhhh...eeeeeee...hhhhhhh.....eeeeeee.....eeeeeeee.hhhhhhhhhhhhhhh..hhhhhhh........hhhhhhhhhh...hhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------PYRIDINE_RE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zk7 A   1 MEPPVQVAVIGSGGAAMAAALKAVEQGAQVTLIERGTIGGTCVNVGCVPSKIMIRAAHIAHLRRESPFDGGIAATVPTIDRSKLLAQQQARVDELRHAKYEGILGGNPAITVVHGEARFKDDQSLTVRLNEGGERVVMFDRCLVATGASPAVPPIPGLKESPYWTSTEALASDTIPERLAVIGSSVVALELAQAFARLGSKVTVLARNTLFFREDPAIGEAVTAAFRAEGIEVLEHTQASQVAHMDGEFVLTTTHGELRADKLLVATGRTPNTRSLALDAAGVTVNAQGAIVIDQGMRTSNPNIYAAGDCTDQPQFVYVAAAAGTRAAINMTGGDAALDLTAMPAVVFTDPQVATVGYSEAEAHHDGIETDSRTLTLDNVPRALANFDTRGFIKLVIEEGSHRLIGVQAVAPEAGELIQTAALAIRNRMTVQELADQLFPYLTMVEGLKLAAQTFNKDVKQLSCCAG 467
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460
   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 1ZK7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZK7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ZK7)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (MERA_PSEAI | P00392)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0016152    mercury (II) reductase activity    Catalysis of the reaction: H(+) + Hg + NADP(+) = Hg(2+) + NADPH.
    GO:0045340    mercury ion binding    Interacting selectively and non-covalently with mercury (Hg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016668    oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0050787    detoxification of mercury ion    Any process that reduce or remove the toxicity of mercuric ion. These include transport of mercury away from sensitive areas and to compartments or complexes whose purpose is sequestration of mercury ion and/or reduction of mercury ion (Hg[II]) to metallic mercury (Hg[0]).
    GO:0030001    metal ion transport    The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0046689    response to mercury ion    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 mercury ion stimulus.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MERA_PSEAI | P00392: 1zx9 2kt2 2kt3 4k7z 4k8d

(-) Related Entries Specified in the PDB File

1ger GLUTATHIONE REDUCTASE, E.COLI
3grs GLUTATHIONE REDUCTASE, HUMAN