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(-) Description

Title :  THE CRYSTAL STRUCTURE OF RHODOBACTER SPHAEROIDES DIMETHYLSULFOXIDE REDUCTASE REVEALS TWO DISTINCT MOLYBDENUM COORDINATION ENVIRONMENTS.
 
Authors :  H. K. Li, K. Temple, K. V. Rajagopalan, H. Schindelin
Date :  13 Apr 00  (Deposition) - 02 Aug 00  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Molybdenum, Molybdenum Cofactor, Dmso, Reductase, Molybdopterin, Mgd, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. K. Li, K. Temple, K. V. Rajagopalan, H. Schindelin
The 1. 3 A Crystal Structure Of Rhodobacter Sphaeroides Dimethylsulfoxide Reductase Reveals Two Distinct Molybdenum Coordination Environments
J. Am. Chem. Soc. V. 122 7673 2000
PubMed: search  |  Reference-DOI: 10.1021/JA000643E
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIMETHYL SULFOXIDE REDUCTASE
    Chains: A
    EC Number: 1.8.99.-
    Engineered: YES
    Expression System: BACTERIA
    Expression System Common: EUBACTERIA
    Expression System Taxid: 2
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Synonym: DMSO REDUCTASE, DMSOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 12)

Asymmetric/Biological Unit (8, 12)
No.NameCountTypeFull Name
16MO1Ligand/IonMOLYBDENUM(VI) ION
2CD1Ligand/IonCADMIUM ION
3CSD1Mod. Amino Acid3-SULFINOALANINE
4EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5GLC3Ligand/IonALPHA-D-GLUCOSE
6MGD2Ligand/Ion2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINEDINUCLEOTIDE
7O2Ligand/IonOXYGEN ATOM
8SO41Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:509 , ALA A:517 , GLU A:520 , GLY A:525 , HOH A:3007 , HOH A:3011 , HOH A:3036 , HOH A:3056 , HOH A:3162 , HOH A:3393 , HOH A:3676 , HOH A:3898BINDING SITE FOR RESIDUE GLC A 2002
02AC2SOFTWAREMET A:9 , TRP A:32 , ASP A:33 , LYS A:34 , LYS A:67 , ASN A:70 , GLU A:565 , ILE A:567 , HOH A:3554 , HOH A:3803 , HOH A:3822 , HOH A:4002BINDING SITE FOR RESIDUE GLC A 2003
03AC3SOFTWAREARG A:401 , ASP A:404 , VAL A:743 , GLY A:744 , GLN A:750 , HOH A:3005 , HOH A:3010 , HOH A:3333 , HOH A:3438 , HOH A:3841 , HOH A:4000BINDING SITE FOR RESIDUE GLC A 2004
04AC4SOFTWARETYR A:278 , SER A:283 , ASP A:284 , HIS A:618 , HOH A:3128 , HOH A:3504 , HOH A:3517 , HOH A:3696 , HOH A:3818BINDING SITE FOR RESIDUE SO4 A 2005
05AC5SOFTWAREASP A:87 , ASP A:91BINDING SITE FOR RESIDUE CD A 2006
06AC6SOFTWARETYR A:114 , GLY A:115 , TRP A:116 , LYS A:117 , SER A:118 , TYR A:146 , SER A:147 , ARG A:326 , GLY A:432 , GLY A:433 , ASN A:434 , HIS A:438 , GLN A:440 , GLN A:458 , ASP A:459 , PHE A:460 , THR A:463 , ALA A:475 , ARG A:481 , ASP A:511 , ALA A:641 , HIS A:643 , LEU A:648 , HIS A:649 , SER A:650 , GLN A:651 , GLU A:715 , ASN A:737 , GLY A:754 , GLN A:755 , MGD A:1002 , 6MO A:3000 , O A:3001 , O A:3002 , HOH A:3205 , HOH A:3232 , HOH A:3295 , HOH A:3304 , HOH A:3678BINDING SITE FOR RESIDUE MGD A 1001
07AC7SOFTWARETRP A:116 , SER A:147 , ALA A:185 , LYS A:190 , THR A:191 , GLU A:193 , ILE A:194 , ILE A:220 , ASN A:221 , PRO A:222 , PRO A:240 , GLN A:241 , ASP A:243 , GLY A:321 , TRP A:322 , SER A:323 , ILE A:324 , ARG A:326 , MET A:327 , HIS A:359 , VAL A:640 , SER A:642 , HIS A:643 , PRO A:644 , LYS A:645 , ARG A:647 , HIS A:649 , GLN A:755 , MGD A:1001 , 6MO A:3000 , O A:3001 , HOH A:3194 , HOH A:3222 , HOH A:3234 , HOH A:3294BINDING SITE FOR RESIDUE MGD A 1002
08AC8SOFTWARETYR A:114 , SER A:147 , MGD A:1001 , MGD A:1002 , EPE A:2001 , O A:3001 , O A:3002BINDING SITE FOR RESIDUE 6MO A 3000
09AC9SOFTWARETYR A:114 , TRP A:116 , SER A:147 , MGD A:1001 , MGD A:1002 , EPE A:2001 , 6MO A:3000 , O A:3002BINDING SITE FOR RESIDUE O A 3001
10BC1SOFTWARETYR A:114 , ASP A:145 , TYR A:146 , SER A:147 , MGD A:1001 , EPE A:2001 , 6MO A:3000 , O A:3001BINDING SITE FOR RESIDUE O A 3002
11BC2SOFTWARETYR A:114 , ASP A:145 , SER A:147 , TYR A:165 , TRP A:196 , TYR A:360 , 6MO A:3000 , O A:3001 , O A:3002 , HOH A:3136 , HOH A:3370 , HOH A:3747BINDING SITE FOR RESIDUE EPE A 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EU1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EU1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EU1)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MOLYBDOPTERIN_PROK_2PS00490 Prokaryotic molybdopterin oxidoreductases signature 2.DSTOR_RHOSH505-522  1A:463-480
2MOLYBDOPTERIN_PROK_3PS00932 Prokaryotic molybdopterin oxidoreductases signature 3.DSTOR_RHOSH718-745  1A:676-703

(-) Exons   (0, 0)

(no "Exon" information available for 1EU1)

(-) 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:767
 aligned with DSTOR_RHOSH | Q57366 from UniProtKB/Swiss-Prot  Length:822

    Alignment length:777
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       
          DSTOR_RHOSH    46 ANGEVMSGCHWGVFKARVENGRAVAFEPWDKDPAPSHQLPGVLDSIYSPTRIKYPMVRREFLEKGVNADRSTRGNGDFVRVTWDEALDLVARELKRVQESYGPTGTFGGSYGWKSPGRLHNCQVLMRRALNLAGGFVNSSGDYSTAAAQIIMPHVMGTLEVYEQQTAWPVVVENTDLMVFWAADPMKTNEIGWVIPDHGAYAGMKALKEKGTRVICINPVRTETADYFGADVVSPRPQTDVALMLGMAHTLYSEDLHDKDFLENCTTGFDLFAAYLTGESDGTPKTAEWAAEICGLPAEQIRELARSFVAGRTMLAAGWSIQRMHHGEQAHWMLVTLASMIGQIGLPGGGFGLSYHYSNGGSPTSDGPALGGISDGGKAVEGAAWLSESGATSIPCARVVDMLLNPGGEFQFNGATATYPDVKLAYWAGGNPFAHHQDRNRMLKAWEKLETFIVQDFQWTATARHADIVLPATTSYERNDIESVGDYSNRAILAMKKVVDPLYEARSDYDIFAALAERLGKGAEFTEGRDEMGWISSFYEAAVKQAEFKNVAMPSFEDFWSEGIVEFPITEGANFVRYADFREDPLFNPLGTPSGLIEIYSKNIEKMGYDDCPAHPTWMEPAERLGGAGAKYPLHVVASHPKSRLHSQLNGTSLRDLYAVAGHEPCLINPADAAARGIADGDVLRVFNDRGQILVGAKVSDAVMPGAIQIYEGGWYDPLDPSEEGTLDKYGDVNVLSLDVGTSKLAQGNCGQTILADVEKYAGAPVTVTVFDTPKGA 822
               SCOP domains d1eu1a2 A:4-625 Dimethylsulfoxide reductase (DMSO reductase)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  d1eu1a1 A:626-780 Dimethylsulfoxide reductase (DMSO reductase)                                                                                              SCOP domains
               CATH domains -1eu1A03                     ---------------------1eu1A01 A:54-145,A:378-481,A:507-529  [code=3.40.50.740, no name defined]                   -1eu1A02 A:147-366,A:579-604 Dimethylsulfoxide Reductase, domain 2                                                                                                                                                           -----------1eu   1A       01 A:54-145,A:378-481,A:507-529  [code=3.40.50.740, no name defined]                     1eu1A03           -------1eu1A01                1eu1A03 A:5-32,A:482-499,A:530-570       --------1eu1A02                   -------1eu1A04 A:612-774  [code=2.40.40.20, no name defined]                                                                                                              ------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeee..eeeeeee.........hhhhhhhh..........eeehhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhh...ee.............hhhhhhhhhhhhhh...eee......hhhhhhhhhh..........hhhhhhhhh.eeeee..hhhhhh........hhhhhhhhhhhhhh.eee......hhhhhhhh.........hhhhhhhhhhhhhhhh...hhhhhhhheehhhhhhhhhh........hhhhhhhhhh.hhhhhhhhhhhhhh..eeeee.hhhhh....hhhhhhhhhhhhhhh.......eee.........................---..-------...eee..hhhhhhhh...eeee..eeee.....eeeee..hhhhhh.hhhhhhhhhhhh.eeeeee...hhhhhh..eeee..hhhhh.eeeee......eeeee...........hhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhheee...hhhhhh..hhhhhhh............ee..hhhhhhhh.........................eeee..............hhhhhhh......eeeehhhhhhh.......eeeee....eeeeeeee.......eee......................hhhhh..................eeeeee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MOLYBDOPTERIN_PROK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MOLYBDOPTERIN_PROK_3        ----------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eu1 A   4 ANGEVMSGCHWGVFKARVENGRAVAFEPWDKDPAPSHQLPGVLDSIYSPTRIKYPMVRREFLEKGVNADRSTRGNGDFVRVTWDEALDLVARELKRVQESYGPTGTFGGSYGWKSPGRLHNCQVLMRRALNLAGGFVNSSGDYSTAAAQIIMPHVMGTLEVYEQQTAWPVVVENTDLMVFWAADPMKTNEIGWVIPDHGAYAGMKALKEKGTRVIcINPVRTETADYFGADVVSPRPQTDVALMLGMAHTLYSEDLHDKDFLENCTTGFDLFAAYLTGESDGTPKTAEWAAEICGLPAEQIRELARSFVAGRTMLAAGWSIQRMHHGEQAHWMLVTLASMIGQIGLPGGGFGLSYHYSNGGSPTSDGPALGGISDGG---EG-------GATSIPCARVVDMLLNPGGEFQFNGATATYPDVKLAYWAGGNPFAHHQDRNRMLKAWEKLETFIVQDFQWTATARHADIVLPATTSYERNDIESVGDYSNRAILAMKKVVDPLYEARSDYDIFAALAERLGKGAEFTEGRDEMGWISSFYEAAVKQAEFKNVAMPSFEDFWSEGIVEFPITEGANFVRYADFREDPLFNPLGTPSGLIEIYSKNIEKMGYDDCPAHPTWMEPAERLGGAGAKYPLHVVASHPKSRLHSQLNGTSLRDLYAVAGHEPCLINPADAAARGIADGDVLRVFNDRGQILVGAKVSDAVMPGAIQIYEGGWYDPLDPSEEGTLDKYGDVNVLSLDVGTSKLAQGNCGQTILADVEKYAGAPVTVTVFDTPKGA 780
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213     | 223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373      |  -||     393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       
                                                                                                                                                                                                                                                 219-CSD                                                                                                                                                          380 384|     393                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                                                       385
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EU1)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DSTOR_RHOSH | Q57366)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030151    molybdenum ion binding    Interacting selectively and non-covalently with molybdenum (Mo) ions.
    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:0050626    trimethylamine-N-oxide reductase (cytochrome c) activity    Catalysis of the reaction: trimethylamine + 2 (ferricytochrome c)-subunit + H2O = trimethylamine-N-oxide + 2 (ferrocytochrome c)-subunit + 2 H+.
biological process
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  DSTOR_RHOSH | Q57366
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1cxs 1cxt