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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MEMBRANE PROXIMAL OXIDOREDUCTASE DOMAIN OF HUMAN STEAP3, THE DOMINANT FERRIC REDUCTASE OF THE ERYTHROID TRANSFERRIN CYCLE
 
Authors :  A. K. Sendamarai, R. S. Ohgami, M. D. Fleming, C. M. Lawrence
Date :  10 Mar 08  (Deposition) - 06 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C#
Biol. Unit 1:  A,B  (1x)
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Metal-Binding, Transmembrane, Rossmann Fold, Transport, Cell Cycle, Transferrin, Flavoprotein, Alternative Splicing, Transferrin Receptor, Ferrireductase, Ferric- Reductase, Iron Transport, Phosphoprotein, Oxidoreductase, Steap3, Copper, Membrane, Endosome, Apoptosis, Tf, Nad, Tfr, Fad, Fno, Nadp, Tfr1, Iron, Steap, Polymorphism, Glycoprotein, Ion Transport, Dinucleotide-Binding Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Sendamarai, R. S. Ohgami, M. D. Fleming, C. M. Lawrence
Structure Of The Membrane Proximal Oxidoreductase Domain Of Human Steap3, The Dominant Ferrireductase Of The Erythroid Transferrin Cycle
Proc. Natl. Acad. Sci. Usa V. 105 7410 2008
PubMed-ID: 18495927  |  Reference-DOI: 10.1073/PNAS.0801318105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METALLOREDUCTASE STEAP3
    Chains: A, B
    EC Number: 1.16.1.2, 1.16.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Expression System Vector Type: PLASMID
    Fragment: NADPH/FLAVIN DEPENDENT OXIDOREDUCTASE, RESIDUES 1-215
    Organ: KIDNEY
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: RESIDUES 1-215 CLONED, NADPH BOUND
    Synonym: STEAP3 DIMER WITH NADPH, SIX-TRANSMEMBRANE EPITHELIAL ANTIGEN OF PROSTATE 3, TUMOR SUPPRESSOR-ACTIVATED PATHWAY PROTEIN 6, HTSAP6, PHYDE, HPHYDE, DUDULIN-2
    Tissue: RENAL CELL ADENOCARCINOMA

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC#
Biological Unit 1 (1x): AB 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:36 , GLY A:37 , ASP A:38 , PHE A:39 , SER A:58 , ARG A:59 , ALA A:90 , VAL A:91 , PHE A:92 , HIS A:95 , SER A:98 , VAL A:114 , SER A:115 , ASN A:116 , ASN A:147 , ILE A:149 , SER A:150 , ALA A:151 , HOH A:2013 , HOH A:2057 , HOH A:2058 , HOH A:2059 , HOH A:2060 , HOH A:2061BINDING SITE FOR RESIDUE NAP A1210
2AC2SOFTWAREGLY B:35 , SER B:36 , GLY B:37 , ASP B:38 , PHE B:39 , SER B:58 , ARG B:59 , ALA B:90 , VAL B:91 , PHE B:92 , HIS B:95 , SER B:98 , VAL B:114 , SER B:115 , ASN B:116 , ILE B:149 , ALA B:151 , HOH B:2014 , HOH B:2023 , HOH B:2058 , HOH B:2060 , HOH B:2061 , HOH B:2062 , HOH B:2063BINDING SITE FOR RESIDUE NAP B1210
3AC3SOFTWARELYS B:62 , ARG B:66 , HOH C:2001BINDING SITE FOR RESIDUE CIT A1211

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VQ3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:29 -Lys A:30
2Asp A:160 -Gly A:161
3Pro B:29 -Lys B:30
4Arg B:207 -Leu B:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_031975A184TSTEA3_HUMANPolymorphism17013371A/BA184T
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_031975A184TSTEA3_HUMANPolymorphism17013371A/BA184T
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VQ3)

(-) Exons   (0, 0)

(no "Exon" information available for 2VQ3)

(-) 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:181
 aligned with STEA3_HUMAN | Q658P3 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:181
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208 
          STEA3_HUMAN    29 PKVGILGSGDFARSLATRLVGSGFKVVVGSRNPKRTARLFPSAAQVTFQEEAVSSPEVIFVAVFREHYSSLCSLSDQLAGKILVDVSNPTEQEHLQHRESNAEYLASLFPTCTVVKAFNVISAWTLQAGPRDGNRQVPICGDQPEAKRAVSEMALAMGFMPVDMGSLASAWEVEAMPLRLL 209
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..hhhhhhhhhhhhhh...eeeee.hhhhhhh......eeeehhhhh....eeee..hhhhhhhhhhhhhhhh..eeee....hhhhhhhh..hhhhhhhhhh...eeeee....hhhhhhhh......eeeeee.hhhhhhhhhhhhhhh..eeee..hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vq3 A  29 PKVGILGSGDFARSLATRLVGSGFKVVVGSRNPKRTARLFPSAAQVTFQEEAVSSPEVIFVAVFREHYSSLCSLSDQLAGKILVDVSNPTEQEHLQHRESNAEYLASLFPTCTVVKAFNVISAWTLQAGPRDGNRQVPICGDQPEAKRAVSEMALAMGFMPVDMGSLASAWEVEAMPLRLL 209
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208 


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with STEA3_HUMAN | Q658P3 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:180
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208
          STEA3_HUMAN    29 PKVGILGSGDFARSLATRLVGSGFKVVVGSRNPKRTARLFPSAAQVTFQEEAVSSPEVIFVAVFREHYSSLCSLSDQLAGKILVDVSNPTEQEHLQHRESNAEYLASLFPTCTVVKAFNVISAWTLQAGPRDGNRQVPICGDQPEAKRAVSEMALAMGFMPVDMGSLASAWEVEAMPLRL 208
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -F420_oxidored-2vq3B01 B:30-117                                                          ------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -F420_oxidored-2vq3B02 B:30-117                                                          ------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeee..hhhhhhhhhhhhhh...eeeee.hhhhhhh......eeeehhhhh....eeee..hhhhhhhhhhhhhhhh..eeee....hhhhhhhh..hhhhhhhhhh...eeeee....hhhhhhhh......eeeeee.hhhhhhhhhhhhhhh..eeee..hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vq3 B  29 PKVGILGSGDFARSLATRLVGSGFKVVVGSRNPKRTARLFPSAAQVTFQEEAVSSPEVIFVAVFREHYSSLCSLSDQLAGKILVDVSNPTEQEHLQHRESNAEYLASLFPTCTVVKAFNVISAWTLQAGPRDGNRQVPICGDQPEAKRAVSEMALAMGFMPVDMGSLASAWEVEAMPLRL 208
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208
   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 2VQ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VQ3)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (STEA3_HUMAN | Q658P3)
molecular function
    GO:0008823    cupric reductase activity    Catalysis of the reaction: Cu+ + NAD+ + H+ = Cu2+ + NADH.
    GO:0052851    ferric-chelate reductase (NADPH) activity    Catalysis of the reaction: 2 Fe3+ + NADPH = 2 Fe2+ + H+ + NADP+ .
    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:0016723    oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor    Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered and NAD+ or NADP+ acts as an electron acceptor.
    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).
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0015677    copper ion import    The directed movement of copper ions into a cell or organelle.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    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:0009306    protein secretion    The controlled release of proteins from a cell.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0033572    transferrin transport    The directed movement of transferrin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    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:0005887    integral component of plasma membrane    The component of the plasma 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.
    GO:0005771    multivesicular body    A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        STEA3_HUMAN | Q658P3: 2vns

(-) Related Entries Specified in the PDB File

2vns CRYSTAL STRUCTURE OF THE MEMBRANE PROXIMAL OXIDOREDUCTASE DOMAIN OF HUMAN STEAP3, THE DOMINANT FERRIC REDUCTASE OF THE ERYTHROID TRANSFERRIN CYCLE