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(-) Description

Title :  CRYSTAL STRUCTURE OF N-ETHYLMALEIMIDINE REDUCTASE FROM BURKHOLDERIA PSEUDOMALLEI
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Date :  10 Mar 09  (Deposition) - 17 Mar 09  (Release) - 17 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Decode Biostructures, Ssgcid, Niaid, Targetdb Bupsa00093A, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Edwards, B. L. Staker, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of N-Ethylmaleimidine Reductase From Burkholderia Pseudomallei
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N-ETHYLMALEIMIDE REDUCTASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: BG1861
    Gene: BPSS0877
    Organism Common: PSEUDOMONAS PSEUDOMALLEI
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 28450
    Strain: 1710B

 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, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:30 , PRO A:31 , LEU A:32 , THR A:33 , ALA A:64 , GLN A:106 , HIS A:181 , ASN A:184 , HIS A:233 , ARG A:270 , ASN A:293 , GLU A:294 , ASN A:295 , TRP A:315 , GLY A:316 , LYS A:317 , TYR A:344 , HOH A:470 , HOH A:476 , HOH A:477 , HOH A:478 , HOH A:512 , HOH A:513BINDING SITE FOR RESIDUE FMN A 362
2AC2SOFTWAREALA B:30 , PRO B:31 , LEU B:32 , THR B:33 , ALA B:64 , GLN B:106 , HIS B:181 , ASN B:184 , HIS B:233 , ARG B:270 , ASN B:293 , GLU B:294 , ASN B:295 , TRP B:315 , GLY B:316 , LYS B:317 , TYR B:344 , HOH B:399 , HOH B:471 , HOH B:472 , HOH B:473BINDING SITE FOR RESIDUE FMN B 362

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:140 -Pro A:141
2Arg B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GKA)

(-) Exons   (0, 0)

(no "Exon" information available for 3GKA)

(-) 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:350
 aligned with Q3JFM9_BURP1 | Q3JFM9 from UniProtKB/TrEMBL  Length:353

    Alignment length:350
                                    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
         Q3JFM9_BURP1     1 MPSLFDPLTIGDLTLANRIIMAPLTRARAGDTRTPNALMARYYAERASAGLIISEATSVTPQGVGYASTPGIWSPEQVDGWRLVTDAVHAAGGRIFLQLWHVGRVSDPVFLDGALPVAPSAIAPGGHVSLVRPQRPYVTPRALELDEIPGVVAAFRRGAENARAAGFDGVEVHGANGYLLDQFLQDSANRRTDAYGGSIENRARLLLEVVDAAIDVWSAARVGVHLAPRGDAHTMGDSDPAATFGHVARELGRRRIAFLFARESFGGDAIGQQLKAAFGGPFIVNENFTLDSAQAALDAGQADAVAWGKLFIANPDLPRRFKLNAPLNEPNAATFYAQGEVGYTDYPALE 350
               SCOP domains d3gkaa_ A: automated matches                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3gkaA00 A:9-358 Aldolase class I                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eee...eee..............hhhhhhhhhh.....eeeeeeee.hhhhh.........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhh.....ee......................ee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhh..eeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhh......hhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gka A   9 MPSLFDPLTIGDLTLANRIIMAPLTRARAGDTRTPNALMARYYAERASAGLIISEATSVTPQGVGYASTPGIWSPEQVDGWRLVTDAVHAAGGRIFLQLWHVGRVSDPVFLDGALPVAPSAIAPGGHVSLVRPQRPYVTPRALELDEIPGVVAAFRRGAENARAAGFDGVEVHGANGYLLDQFLQDSANRRTDAYGGSIENRARLLLEVVDAAIDVWSAARVGVHLAPRGDAHTMGDSDPAATFGHVARELGRRRIAFLFARESFGGDAIGQQLKAAFGGPFIVNENFTLDSAQAALDAGQADAVAWGKLFIANPDLPRRFKLNAPLNEPNAATFYAQGEVGYTDYPALE 358
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358


Chain A from PDB  Type:PROTEIN  Length:350
 aligned with Q63LY5_BURPS | Q63LY5 from UniProtKB/TrEMBL  Length:353

    Alignment length:350
                                    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
         Q63LY5_BURPS     1 MPSLFDPLTIGDLTLANRIIMAPLTRARAGDTRTPNALMARYYAERASAGLIISEATSVTPQGVGYASTPGIWSPEQVDGWRLVTDAVHAAGGRIFLQLWHVGRVSDPVFLDGALPVAPSAIAPGGHVSLVRPQRPYVTPRALELDEIPGVVAAFRRGAENARAAGFDGVEVHGANGYLLDQFLQDSANRRTDAYGGSIENRARLLLEVVDAAIDVWSAARVGVHLAPRGDAHTMGDSDPAATFGHVARELGRRRIAFLFARESFGGDAIGQQLKAAFGGPFIVNENFTLDSAQAALDAGQADAVAWGKLFIANPDLPRRFKLNAPLNEPNAATFYAQGEVGYTDYPALE 350
               SCOP domains d3gkaa_ A: automated matches                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3gkaA00 A:9-358 Aldolase class I                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eee...eee..............hhhhhhhhhh.....eeeeeeee.hhhhh.........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhh.....ee......................ee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhh..eeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhh......hhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gka A   9 MPSLFDPLTIGDLTLANRIIMAPLTRARAGDTRTPNALMARYYAERASAGLIISEATSVTPQGVGYASTPGIWSPEQVDGWRLVTDAVHAAGGRIFLQLWHVGRVSDPVFLDGALPVAPSAIAPGGHVSLVRPQRPYVTPRALELDEIPGVVAAFRRGAENARAAGFDGVEVHGANGYLLDQFLQDSANRRTDAYGGSIENRARLLLEVVDAAIDVWSAARVGVHLAPRGDAHTMGDSDPAATFGHVARELGRRRIAFLFARESFGGDAIGQQLKAAFGGPFIVNENFTLDSAQAALDAGQADAVAWGKLFIANPDLPRRFKLNAPLNEPNAATFYAQGEVGYTDYPALE 358
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358


Chain B from PDB  Type:PROTEIN  Length:351
 aligned with Q3JFM9_BURP1 | Q3JFM9 from UniProtKB/TrEMBL  Length:353

    Alignment length:351
                             1                                                                                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349 
         Q3JFM9_BURP1     - -MPSLFDPLTIGDLTLANRIIMAPLTRARAGDTRTPNALMARYYAERASAGLIISEATSVTPQGVGYASTPGIWSPEQVDGWRLVTDAVHAAGGRIFLQLWHVGRVSDPVFLDGALPVAPSAIAPGGHVSLVRPQRPYVTPRALELDEIPGVVAAFRRGAENARAAGFDGVEVHGANGYLLDQFLQDSANRRTDAYGGSIENRARLLLEVVDAAIDVWSAARVGVHLAPRGDAHTMGDSDPAATFGHVARELGRRRIAFLFARESFGGDAIGQQLKAAFGGPFIVNENFTLDSAQAALDAGQADAVAWGKLFIANPDLPRRFKLNAPLNEPNAATFYAQGEVGYTDYPALE 350
               SCOP domains d3gkab_ B: automated matches                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3gkaB00 B:8-358 Aldolase class I                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eee...eee..............hhhhhhhhhh.....eeeeeeee.hhhhh.........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhh.....ee......................ee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhh..eeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhh.......hhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gka B   8 HMPSLFDPLTIGDLTLANRIIMAPLTRARAGDTRTPNALMARYYAERASAGLIISEATSVTPQGVGYASTPGIWSPEQVDGWRLVTDAVHAAGGRIFLQLWHVGRVSDPVFLDGALPVAPSAIAPGGHVSLVRPQRPYVTPRALELDEIPGVVAAFRRGAENARAAGFDGVEVHGANGYLLDQFLQDSANRRTDAYGGSIENRARLLLEVVDAAIDVWSAARVGVHLAPRGDAHTMGDSDPAATFGHVARELGRRRIAFLFARESFGGDAIGQQLKAAFGGPFIVNENFTLDSAQAALDAGQADAVAWGKLFIANPDLPRRFKLNAPLNEPNAATFYAQGEVGYTDYPALE 358
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357 


Chain B from PDB  Type:PROTEIN  Length:351
 aligned with Q63LY5_BURPS | Q63LY5 from UniProtKB/TrEMBL  Length:353

    Alignment length:351
                             1                                                                                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349 
         Q63LY5_BURPS     - -MPSLFDPLTIGDLTLANRIIMAPLTRARAGDTRTPNALMARYYAERASAGLIISEATSVTPQGVGYASTPGIWSPEQVDGWRLVTDAVHAAGGRIFLQLWHVGRVSDPVFLDGALPVAPSAIAPGGHVSLVRPQRPYVTPRALELDEIPGVVAAFRRGAENARAAGFDGVEVHGANGYLLDQFLQDSANRRTDAYGGSIENRARLLLEVVDAAIDVWSAARVGVHLAPRGDAHTMGDSDPAATFGHVARELGRRRIAFLFARESFGGDAIGQQLKAAFGGPFIVNENFTLDSAQAALDAGQADAVAWGKLFIANPDLPRRFKLNAPLNEPNAATFYAQGEVGYTDYPALE 350
               SCOP domains d3gkab_ B: automated matches                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3gkaB00 B:8-358 Aldolase class I                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eee...eee..............hhhhhhhhhh.....eeeeeeee.hhhhh.........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhh.....ee......................ee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhh..eeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhh.......hhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gka B   8 HMPSLFDPLTIGDLTLANRIIMAPLTRARAGDTRTPNALMARYYAERASAGLIISEATSVTPQGVGYASTPGIWSPEQVDGWRLVTDAVHAAGGRIFLQLWHVGRVSDPVFLDGALPVAPSAIAPGGHVSLVRPQRPYVTPRALELDEIPGVVAAFRRGAENARAAGFDGVEVHGANGYLLDQFLQDSANRRTDAYGGSIENRARLLLEVVDAAIDVWSAARVGVHLAPRGDAHTMGDSDPAATFGHVARELGRRRIAFLFARESFGGDAIGQQLKAAFGGPFIVNENFTLDSAQAALDAGQADAVAWGKLFIANPDLPRRFKLNAPLNEPNAATFYAQGEVGYTDYPALE 358
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357
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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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q3JFM9_BURP1 | Q3JFM9)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
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.

Chain A,B   (Q63LY5_BURPS | Q63LY5)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
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.

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 Related Entries

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