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(-) Description

Title :  CRYSTAL STRUCTURE OF WT MAUG IN COMPLEX WITH PRE-METHYLAMINE DEHYDROGENASE AGED 60 DAYS
 
Authors :  E. T. Yukl, C. M. Wilmot
Date :  22 May 12  (Deposition) - 27 Mar 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Trytpophan Tryptophylquinone, Oxidoreductase-Electron Transfe Complex, Oxidoreductase-Electron Transfer Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. T. Yukl, F. Liu, J. Krzystek, S. Shin, L. M. Jensen, V. L. Davidson, C. M. Wilmot, A. Liu
Diradical Intermediate Within The Context Of Tryptophan Tryptophylquinone Biosynthesis.
Proc. Natl. Acad. Sci. Usa V. 110 4569 2013
PubMed-ID: 23487750  |  Reference-DOI: 10.1073/PNAS.1215011110

(-) Compounds

Molecule 1 - METHYLAMINE UTILIZATION PROTEIN MAUG
    Chains: A, B
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: PARACOCCUS DENITRIFICANS
    Expression System Taxid: 266
    Fragment: UNP RESIDUES 21-387
    Gene: MAUG, PDEN_4736
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 318586
    Strain: PD 1222
 
Molecule 2 - METHYLAMINE DEHYDROGENASE LIGHT CHAIN
    Chains: C, E
    EC Number: 1.4.9.1
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Taxid: 1063
    Fragment: UNP RESIDUES 58-188
    Gene: MAUA
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 266
    Synonym: MADH, METHYLAMINE DEHYDROGENASE (AMICYANIN)
 
Molecule 3 - METHYLAMINE DEHYDROGENASE HEAVY CHAIN
    Chains: D, F
    EC Number: 1.4.99.3
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Taxid: 1063
    Fragment: UNP RESIDUES 33-417
    Gene: PDEN_4730
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 318586
    Strain: PD 1222

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
10AF2Mod. Amino Acid7-HYDROXY-L-TRYPTOPHAN
2CA2Ligand/IonCALCIUM ION
3HEC4Ligand/IonHEME C
4MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5NA3Ligand/IonSODIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:66 , THR A:275 , PRO A:277 , HOH A:514 , HOH A:523 , HOH A:545 , HOH A:572BINDING SITE FOR RESIDUE CA A 401
02AC2SOFTWAREGLN A:29 , SER A:30 , CYS A:31 , CYS A:34 , HIS A:35 , SER A:54 , VAL A:55 , ARG A:65 , THR A:67 , PRO A:68 , LEU A:70 , GLN A:91 , PHE A:92 , TRP A:93 , ARG A:96 , LEU A:100 , GLN A:103 , ALA A:104 , PRO A:107 , GLU A:113 , MET A:114 , GLN A:163 , LYS A:265BINDING SITE FOR RESIDUE HEC A 402
03AC3SOFTWARETRP A:93 , ASN A:200 , CYS A:201 , CYS A:204 , HIS A:205 , HIS A:224 , LEU A:228 , PHE A:264 , PRO A:267 , VAL A:272 , TYR A:278 , MET A:279 , HIS A:280 , LEU A:287 , TYR A:294 , GLU A:327 , LEU A:334 , HOH A:520 , HOH A:540 , HOH A:545 , HOH A:565BINDING SITE FOR RESIDUE HEC A 403
04AC4SOFTWARELEU A:250 , ARG A:252 , ILE A:255BINDING SITE FOR RESIDUE NA A 404
05AC5SOFTWAREASN B:66 , THR B:275 , PRO B:277 , HOH B:508 , HOH B:510 , HOH B:521 , HOH B:598BINDING SITE FOR RESIDUE CA B 401
06AC6SOFTWAREGLN B:29 , SER B:30 , CYS B:31 , CYS B:34 , HIS B:35 , SER B:54 , ARG B:65 , THR B:67 , PRO B:68 , LEU B:70 , GLN B:91 , PHE B:92 , TRP B:93 , ARG B:96 , LEU B:100 , GLN B:103 , ALA B:104 , PRO B:107 , GLU B:113 , MET B:114 , GLN B:163 , LYS B:265 , HOH B:618 , HOH B:636 , HOH B:640BINDING SITE FOR RESIDUE HEC B 402
07AC7SOFTWARETRP B:93 , ASN B:200 , CYS B:201 , CYS B:204 , HIS B:205 , HIS B:224 , ILE B:226 , LEU B:228 , PHE B:264 , VAL B:266 , PRO B:267 , TYR B:278 , MET B:279 , HIS B:280 , LEU B:287 , TYR B:294 , SER B:324 , GLU B:327 , LEU B:334 , HOH B:508 , HOH B:510 , HOH B:514 , HOH B:562 , HOH B:566BINDING SITE FOR RESIDUE HEC B 403
08AC8SOFTWARELEU B:250 , ARG B:252 , ILE B:255BINDING SITE FOR RESIDUE NA B 404
09AC9SOFTWAREASN B:231 , THR B:233 , HOH B:609BINDING SITE FOR RESIDUE NA B 405
10BC1SOFTWAREALA A:138 , GLY A:141 , ARG D:35 , LEU D:37 , GLU D:38BINDING SITE FOR RESIDUE MES D 401
11BC2SOFTWARELEU B:139 , PHE B:140 , ARG F:35 , LEU F:37 , GLU F:38BINDING SITE FOR RESIDUE MES F 401

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1C:23 -C:88
2C:29 -C:61
3C:36 -C:121
4C:38 -C:86
5C:46 -C:77
6C:78 -C:109
7D:181 -D:196
8E:23 -E:88
9E:29 -E:61
10E:36 -E:121
11E:38 -E:86
12E:46 -E:77
13E:78 -E:109
14F:181 -F:196

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:276 -Pro A:277
2Gly B:276 -Pro B:277
3Ser D:157 -Pro D:158
4Ser F:157 -Pro F:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FB1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FB1)

(-) Exons   (0, 0)

(no "Exon" information available for 4FB1)

(-) 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:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............................hhhhh...ee.....ee..........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.....hhhhhhhhhhhhhhhhhhh..................ee......hhhhhhhhh.......hhhhhh....hhhhh..ee.....hhhhh..........hhhhhhhhhhhhh..hhhhhh.................hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fb1 A   6 ADDALAALGAQLFVDPALSRNATQSCATCHDPARAFTDPREGKAGLAVSVGDDGQSHGDRNTPTLGYAALVPAFHRDANGKYKGGQFWDGRADDLKQQAGQPMLNPVEMAMPDRAAVAARLRDDPAYRTGFEALFGKGVLDDPERAFDAAAEALAAYQATGEFSPFDSKYDRVMRGEEKFTPLEEFGYTVFITWNCRLCHMQRKQGVAERETFTNFEYHNIGLPVNETAREASGLGADHVDHGLLARPGIEDPAQSGRFKVPSLRNVAVTGPYMHNGVFTDLRTAILFYNKYTSRRPEAKINPETGAPWGEPEVARNLSLAELQSGLMLDDGRVDALVAFLETLTDRRYEPLLE 359
                                    15        25        35        45        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    


Chain B from PDB  Type:PROTEIN  Length:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............................hhhhh...ee.....ee..........hhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhh..................ee......hhhhhhhhh.......hhhhhh....hhhhh..ee.....hhhhh..........hhhhhhhhhhhhh..hhhhhh.................hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fb1 B   6 ADDALAALGAQLFVDPALSRNATQSCATCHDPARAFTDPREGKAGLAVSVGDDGQSHGDRNTPTLGYAALVPAFHRDANGKYKGGQFWDGRADDLKQQAGQPMLNPVEMAMPDRAAVAARLRDDPAYRTGFEALFGKGVLDDPERAFDAAAEALAAYQATGEFSPFDSKYDRVMRGEEKFTPLEEFGYTVFITWNCRLCHMQRKQGVAERETFTNFEYHNIGLPVNETAREASGLGADHVDHGLLARPGIEDPAQSGRFKVPSLRNVAVTGPYMHNGVFTDLRTAILFYNKYTSRRPEAKINPETGAPWGEPEVARNLSLAELQSGLMLDDGRVDALVAFLETLTDRRYEPLLEESR 362
                                    15        25        35        45        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       


Chain C from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains d4fb1c_ C: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhh..eee.hhhhh..........eeeeeeeeeeee......eeeeeeeeee........eee.........hhhhh........hhhhh..eeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fb1 C   7 TDPRAKWVPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASwVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKAS 131
                                    16        26        36        46        56|       66        76        86        96       106       116       126     
                                                                             57-0AF                                                                      


Chain D from PDB  Type:PROTEIN  Length:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh................eeeeeehhhhh..eeeeeee....eeeeeeee....eeee......eeeeeeeeee..eeeeeeeeeee......eeeeeee..........hhh.eee.....eeeeee.....eeeeee....eeeeeee...eeeeeeee..eeeeee....eeeee.......eeee...............eee....eeeee....eeeeee......ee...ee..hhhhhhh.eee.....eeee....eeeeeeee.........eeeeeeee.....eeeeeeeeeee.eeee......eeeeee....eeeeee.....eeeee........eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fb1 D  11 QETQGQAAARAAAADLAAGQDDEPRILEAPAPDARRVYVNDPAHFAAVTQQFVIDGEAGRVIGMIDGGFLPNPVVADDGSFIAHASTVFSRIARGERTDYVEVFDPVTLLPTADIELPDAPRFLVGTYPWMTSLTPDGKTLLFYQFSPAPAVGVVDLEGKAFKRMLDVPDCYHIFPTAPDTFFMHCRDGSLAKVAFGTEGTPEITHTEVFHPEDEFLINHPAYSQKAGRLVWPTYTGKIHQIDLSSGDAKFLPAVEALTEAERADGWRPGGWQQVAYHRALDRIYLLVDQRDEWRHKTASRFVVVLDAKTGERLAKFEMGHEIDSINVSQDEKPLLYALSTGDKTLYIHDAESGEELRSVNQLGHGPQVITTADMG 386
                                    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      


Chain E from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains d4fb1e_ E: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhh..eee.hhhhh..........ee.....eeeee......eeeee.eeee........eee.........hhhhh........hhhhh..eeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fb1 E   7 TDPRAKWVPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASwVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKAS 131
                                    16        26        36        46        56|       66        76        86        96       106       116       126     
                                                                             57-0AF                                                                      


Chain F from PDB  Type:PROTEIN  Length:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.................eeeeeehhhhh..eeeeeee....eeeeeeee....eeee......eeeeeeeeeeeeeeeeeeeeeee......eeeeeee..........hhh.eee.....eeeeee.....eeeeee....eeeeeee...eeeeeeee..eeeeee....eeeee.......eeee...............eee....eeeee....eeeeee......ee...ee..hhhhhhh.eee.....eeee....eeeeeeee.........eeeeeeee.....eeeeeeeeeee.eeee......eeeeee....eeeeee.....eeeee........eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fb1 F  11 QETQGQAAARAAAADLAAGQDDEPRILEAPAPDARRVYVNDPAHFAAVTQQFVIDGEAGRVIGMIDGGFLPNPVVADDGSFIAHASTVFSRIARGERTDYVEVFDPVTLLPTADIELPDAPRFLVGTYPWMTSLTPDGKTLLFYQFSPAPAVGVVDLEGKAFKRMLDVPDCYHIFPTAPDTFFMHCRDGSLAKVAFGTEGTPEITHTEVFHPEDEFLINHPAYSQKAGRLVWPTYTGKIHQIDLSSGDAKFLPAVEALTEAERADGWRPGGWQQVAYHRALDRIYLLVDQRDEWRHKTASRFVVVLDAKTGERLAKFEMGHEIDSINVSQDEKPLLYALSTGDKTLYIHDAESGEELRSVNQLGHGPQVITTADMG 386
                                    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
   Legend:   → Mismatch (orange background)
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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/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FB1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FB1)

(-) Gene Ontology  (12, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  4fb1
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 Related Entries

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

UniProtKB/Swiss-Prot
        DHML_PARDE | P22619: 1mg2 1mg3 2bbk 2gc4 2gc7 2j55 2j56 2j57 2mta 3l4m 3l4o 3orv 3pxs 3pxt 3pxw 3rlm 3rmz 3rn0 3sjl 3sle 3svw 3sws 3sxt 4fa1 4fa4 4fa5 4fa9 4fan 4fav 4k3i 4y5r
        MAUG_PARDP | Q51658: 3l4m 3l4o 3orv 3pxs 3pxt 3pxw 3rlm 3rmz 3rn0 3rn1 3sjl 3sle 3svw 3sws 3sxt 4fa1 4fa4 4fa5 4fa9 4fan 4fav 4k3i 4l1q 4l3g 4l3h 4o1q 4y5r
UniProtKB/TrEMBL
        A1BB97_PARDP | A1BB97: 3l4m 3l4o 3orv 3pxs 3pxt 3pxw 3rlm 3rmz 3rn0 3rn1 3sjl 3sle 3svw 3sws 3sxt 4fa1 4fa4 4fa5 4fa9 4fan 4fav 4k3i 4l1q 4l3g 4l3h 4o1q 4y5r

(-) Related Entries Specified in the PDB File

3l4m CRYSTAL STRUCTURE OF WT MAUG IN COMPLEX WITH PRE- METHYLAMINE DEHYDROGENASE
4fa4
4fa5
4fa9
4fan
4fav