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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CARBONYL REDUCTASE 1 IN COMPLEX WITH GLUTATHIONE
 
Authors :  D. Rauh, R. L. Bateman, K. M. Shokat
Date :  28 Nov 07  (Deposition) - 21 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Nadp (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. L. Bateman, D. Rauh, B. Tavshanjian, K. M. Shokat
Human Carbonyl Reductase 1 Is An S-Nitrosoglutathione Reductase
J. Biol. Chem. V. 283 35756 2008
PubMed-ID: 18826943  |  Reference-DOI: 10.1074/JBC.M807125200

(-) Compounds

Molecule 1 - CARBONYL REDUCTASE [NADPH] 1
    ChainsA
    EC Number1.1.1.184
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11B
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCBR1, CBR, CRN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNADPH-DEPENDENT CARBONYL REDUCTASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 13)

Asymmetric/Biological Unit (6, 13)
No.NameCountTypeFull Name
1AB32Ligand/Ion3-(4-AMINO-1-TERT-BUTYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-3-YL)PHENOL
2GOL1Ligand/IonGLYCEROL
3GSH1Ligand/IonGLUTATHIONE
4NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
5P332Ligand/Ion3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
6SO46Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:64 , THR A:163 , ARG A:209 , HOH A:380 , HOH A:387 , HOH A:471BINDING SITE FOR RESIDUE SO4 A 310
02AC2SOFTWARELYS A:216 , GLY A:217 , ASP A:218 , LYS A:219 , HOH A:327 , HOH A:371BINDING SITE FOR RESIDUE SO4 A 311
03AC3SOFTWAREARG A:57 , PHE A:58 , HOH A:476BINDING SITE FOR RESIDUE SO4 A 313
04AC4SOFTWARELYS A:14 , GLY A:15 , HOH A:331 , HOH A:358BINDING SITE FOR RESIDUE SO4 A 314
05AC5SOFTWARESER A:2 , GLY A:3 , GLN A:47 , GLN A:50 , LYS A:129 , HOH A:522BINDING SITE FOR RESIDUE SO4 A 319
06AC6SOFTWAREARG A:41 , ARG A:118 , HOH A:402 , HOH A:451 , HOH A:459BINDING SITE FOR RESIDUE SO4 A 320
07AC7SOFTWARESER A:139 , ILE A:140 , MET A:141 , TYR A:193 , GLY A:228 , TRP A:229 , HOH A:394 , HOH A:423BINDING SITE FOR RESIDUE AB3 A 307
08AC8SOFTWAREARG A:22 , ARG A:26 , ILE A:140 , ARG A:144 , GLU A:244 , HOH A:490 , HOH A:555BINDING SITE FOR RESIDUE AB3 A 308
09AC9SOFTWAREGLY A:11 , ASN A:13 , LYS A:14 , GLY A:15 , ILE A:16 , ARG A:37 , LEU A:61 , ASP A:62 , ILE A:63 , ASP A:64 , ASN A:89 , ALA A:90 , GLY A:91 , ILE A:92 , SER A:138 , TYR A:193 , LYS A:197 , PRO A:227 , GLY A:228 , TRP A:229 , THR A:232 , ASP A:233 , MET A:234 , ALA A:235 , HOH A:322 , HOH A:323 , HOH A:331 , HOH A:334 , HOH A:338 , HOH A:345 , HOH A:360 , HOH A:404 , HOH A:427 , HOH A:545 , HOH A:546BINDING SITE FOR RESIDUE NAP A 309
10BC1SOFTWAREPHE A:94 , LYS A:95 , PHE A:102 , GLN A:105 , SER A:191 , ALA A:192 , TYR A:193 , MET A:234 , HOH A:340 , HOH A:367 , HOH A:406 , HOH A:435 , HOH A:470 , HOH A:492 , HOH A:518BINDING SITE FOR RESIDUE GSH A 315
11BC2SOFTWAREALA A:93 , THR A:122 , LEU A:125 , HIS A:207 , LYS A:210 , GLN A:214 , HOH A:487 , HOH A:488 , HOH A:533BINDING SITE FOR RESIDUE P33 A 316
12BC3SOFTWAREGLN A:60 , SER A:68 , LYS A:156 , GLU A:166 , LEU A:170BINDING SITE FOR RESIDUE P33 A 317
13BC4SOFTWARECYS A:25 , ARG A:26 , PHE A:28 , SER A:29 , GLN A:184BINDING SITE FOR RESIDUE GOL A 318

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:262 -Pro A:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_059053V88ICBR1_HUMANPolymorphism1143663AV87I
2UniProtVAR_031706P131SCBR1_HUMANPolymorphism41557318AP130S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.CBR1_HUMAN181-209  1A:180-208

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002903491aENSE00002172104chr21:37442239-37442702464CBR1_HUMAN1-97971A:2-9695
1.2aENST000002903492aENSE00001044165chr21:37443248-37443355108CBR1_HUMAN97-133371A:96-13237
1.3cENST000002903493cENSE00001044162chr21:37444744-37445464721CBR1_HUMAN133-2771451A:132-276145

(-) 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:275
 aligned with CBR1_HUMAN | P16152 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:275
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272     
           CBR1_HUMAN     3 SGIHVALVTGGNKGIGLAIVRDLCRLFSGDVVLTARDVTRGQAAVQQLQAEGLSPRFHQLDIDDLQSIRALRDFLRKEYGGLDVLVNNAGIAFKVADPTPFHIQAEVTMKTNFFGTRDVCTELLPLIKPQGRVVNVSSIMSVRALKSCSPELQQKFRSETITEEELVGLMNKFVEDTKKGVHQKEGWPSSAYGVTKIGVTVLSRIHARKLSEQRKGDKILLNACCPGWVRTDMAGPKATKSPEEGAETPVYLALLPPDAEGPHGQFVSEKRVEQW 277
               SCOP domains d3bhja_ A: Carbonyl reductase/20beta-hydroxysteroid dehydrogenase                                                                                                                                                                                                                   SCOP domains
               CATH domains 3bhjA00 A:2-276 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhh.eeeeee............hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee...............hhhhhhhhhhhhhh...........eee..eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------I------------------------------------------S-------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:180-208    -------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:2-96 UniProt: 1-97 [INCOMPLETE]                                              -----------------------------------Exon 1.3c  PDB: A:132-276 UniProt: 133-277                                                                                                        Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------Exon 1.2a  PDB: A:96-132             ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3bhj A   2 SGIHVALVTGGNKGIGLAIVRDLCRLFSGDVVLTARDVTRGQAAVQQLQAEGLSPRFHQLDIDDLQSIRALRDFLRKEYGGLDVLVNNAGIAFKVADPTPFHIQAEVTMKTNFFGTRDVCTELLPLIKPQGRVVNVSSIMSVRALKSCSPELQQKFRSETITEEELVGLMNKFVEDTKKGVHQKEGWPSSAYGVTKIGVTVLSRIHARKLSEQRKGDKILLNACCPGWVRTDMAGPKATKSPEEGAETPVYLALLPPDAEGPHGQFVSEKRVEQW 276
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271     

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBR1_HUMAN | P16152)
molecular function
    GO:0047021    15-hydroxyprostaglandin dehydrogenase (NADP+) activity    Catalysis of the reaction: NADP(+) + prostaglandin E(1) = 15-dehydro-prostaglandin E1 + H(+) + NADPH.
    GO:0004090    carbonyl reductase (NADPH) activity    Catalysis of the reaction: R-CHOH-R' + NADP+ = R-CO-R' + NADPH + H+.
    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:0016655    oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
    GO:0050221    prostaglandin-E2 9-reductase activity    Catalysis of the reaction: (5Z,13E)-(15S)-9-alpha,11-alpha,15-trihydroxyprosta-5,13-dienoate + NADP+ = (5Z,13E)-(15S)-11-alpha,15-dihydroxy-9-oxoprosta-5,13-dienoate + NADPH.
biological process
    GO:0019371    cyclooxygenase pathway    The chemical reactions and pathways by which prostaglandins are formed from arachidonic acid, and in which prostaglandin-endoperoxide synthase (cyclooxygenase) catalyzes the committed step in the conversion of arachidonic acid to the prostaglandin-endoperoxides PGG2 and PGH2.
    GO:0017144    drug metabolic process    The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice.
    GO:0030855    epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
    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:0042373    vitamin K metabolic process    The chemical reactions and pathways involving any of the forms of vitamin K, quinone-derived vitamins which are involved in the synthesis of blood-clotting factors in mammals. Vitamin K substances share a methylated naphthoquinone ring structure and vary in the aliphatic side chains attached to the molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:1903561    extracellular vesicle    Any vesicle that is part of the extracellular region.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBR1_HUMAN | P161521wma 2pfg 3bhi 3bhm 4z3d

(-) Related Entries Specified in the PDB File

1wma 2pfg 3bhi 3bhm