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(-) Description

Title :  CRYSTAL STRUCTURE OF ARSAB IN COMPLEX WITH 5,6-DIMETHYLBENZIMIDAZOLE
 
Authors :  S. A. Newmister, C. H. Chan, J. C. Escalante-Semerena, I. Rayment
Date :  02 Oct 12  (Deposition) - 24 Oct 12  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Newmister, C. H. Chan, J. C. Escalante-Semerena, I. Rayment
Structural Insights Into The Function Of The Nicotinate Mononucleotide:Phenol/P-Cresol Phosphoribosyltransferase (Arsab) Enzyme From Sporomusa Ovata.
Biochemistry V. 51 8571 2012
PubMed-ID: 23039029  |  Reference-DOI: 10.1021/BI301142H

(-) Compounds

Molecule 1 - ARSA
    Chains: A, C
    EC Number: 2.4.2.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PARSAB22
    Expression System Strain: JE13607
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ARSA
    Organism Scientific: SPOROMUSA OVATA
    Organism Taxid: 2378
 
Molecule 2 - ARSB
    Chains: B, D
    EC Number: 2.4.2.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PARSAB22
    Expression System Strain: JE13607
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ARSB
    Organism Scientific: SPOROMUSA OVATA
    Organism Taxid: 2378

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1DMD2Ligand/Ion5,6-DIMETHYLBENZIMIDAZOLE
2EDO13Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1DMD1Ligand/Ion5,6-DIMETHYLBENZIMIDAZOLE
2EDO6Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1DMD1Ligand/Ion5,6-DIMETHYLBENZIMIDAZOLE
2EDO7Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:79 , THR A:83 , MET A:87 , MET A:177 , LEU A:317 , GLU A:319 , HOH A:901 , LYS B:29 , PRO B:30 , PHE B:327BINDING SITE FOR RESIDUE DMD A 801
02AC2SOFTWAREGLY A:178 , GLY A:180 , ASN A:181 , THR A:182BINDING SITE FOR RESIDUE EDO A 802
03AC3SOFTWAREPHE A:105 , HIS B:319 , EDO B:405 , HOH B:520 , HOH B:605 , HOH B:811BINDING SITE FOR RESIDUE EDO B 401
04AC4SOFTWAREHOH A:1053 , PHE B:276 , ALA B:277 , ALA B:278 , GLN B:296 , LEU B:297 , LYS B:298BINDING SITE FOR RESIDUE EDO B 402
05AC5SOFTWAREILE B:160 , HOH B:601 , HIS D:39 , HOH D:521 , HOH D:658BINDING SITE FOR RESIDUE EDO B 403
06AC6SOFTWAREARG B:124 , LYS B:125 , LYS B:126 , HOH B:537 , HOH B:666BINDING SITE FOR RESIDUE EDO B 404
07AC7SOFTWAREPHE A:105 , ASP A:328 , HIS B:100 , VAL B:101 , SER B:312 , ASN B:315 , EDO B:401 , HOH B:674BINDING SITE FOR RESIDUE EDO B 405
08AC8SOFTWARETYR C:79 , THR C:83 , MET C:87 , MET C:177 , LEU C:317 , GLU C:319 , HOH C:904 , LYS D:29 , PRO D:30 , PHE D:327BINDING SITE FOR RESIDUE DMD C 801
09AC9SOFTWAREGLY C:178 , GLY C:180 , ASN C:181 , THR C:182BINDING SITE FOR RESIDUE EDO C 802
10BC1SOFTWAREGLU C:176 , ASP C:265 , GLY C:266 , LEU C:267 , ASN C:268 , THR C:269 , GLY C:318 , HOH C:905BINDING SITE FOR RESIDUE EDO C 803
11BC2SOFTWAREPHE C:105 , HIS D:319 , EDO D:404 , HOH D:594 , HOH D:750BINDING SITE FOR RESIDUE EDO D 401
12BC3SOFTWAREPHE D:276 , LEU D:286 , VAL D:291 , PRO D:292 , ALA D:293 , HOH D:513 , HOH D:514 , HOH D:591BINDING SITE FOR RESIDUE EDO D 402
13BC4SOFTWAREHOH C:986 , PHE D:276 , ALA D:277 , ALA D:278 , GLN D:296 , LEU D:297 , LYS D:298BINDING SITE FOR RESIDUE EDO D 403
14BC5SOFTWAREPHE C:105 , ASP C:328 , HIS D:100 , VAL D:101 , SER D:312 , ASN D:315 , EDO D:401 , HOH D:687BINDING SITE FOR RESIDUE EDO D 404
15BC6SOFTWAREASN B:50 , ARG B:54 , HOH B:592 , HOH B:632 , ILE D:261 , LEU D:288 , LEU D:289 , ASP D:290BINDING SITE FOR RESIDUE EDO D 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HDR)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Met A:1 -Ser A:2
2Pro B:193 -Gly B:194
3Pro D:193 -Gly D:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HDR)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4hdra_ A: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......eeeeeeeee.hhhhhhh......hhhhhhhhhhhh...hhhhhhhhhh..eeeeeeee...........ee................hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh.hhhhhhh.......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhh.hhhh.ee......hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hdr A   1 MSLLQATVAKIMRPDTVIKDQVKTKLAGVLQSAGSLGRLEDMVEQYAGITGELNPALPKPCMVVASADHGVARRVVSAYPIETTIHMTANYLISQGASANAFANFCGADMVVVDMGVAGDLSYVPGLWHRKIAYGTQDFTEGPAMTREQAIQAVETGIDIVNDRVKHGNRCFCLGEMGIGNTTSSATIVGAFTGLAPEKVTGRGTGRLKTKMEIVGRALAVNKPNPQDGLDVLAKVGGFELGALAGVILGSAANRCAVVIDGLNTTAAALIANVIHPLSKEYMFASHLSGEPAHSIALRQLQLEACLELGVRLGEGIGASMVVDMLYVAIKLLNN 339
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     ||214       224       234       244       254       264       274       284       294       304       314       324       334     
                                                                                                                                                                                                                                       206|                                                                                                                                
                                                                                                                                                                                                                                        211                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4hdrb_ B: automated matches                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhh........eeeeeeee.......hhhhhhhhhhh..hhhhhhhhhhheeeeeeeee..........eee................hhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh.hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hdr B   1 MLEELIAAIKPLDSIAMEQCQRRVDNLTKPLNSLHSFEHIACKLAGISGNPRPRALEKSIIIMAADNGVAQMTTAARLTGFCQGQAPIQVFAAHVQARLIMVDIGVAADLPHSPAVCRKKLAYGSRNSTEGPAMTRQQAIQAIEVGVRIAQAEIARGCQVIGLGEMGLGGLAAAMAIVACCHGQPLPGLAGREAELVNTAIAVNRPNAADPLDILTKVGGLAIAGLVGVILGAAAGRAAVVLDGLATSTAALIAINLVPDVKPYLIGSHFAAEPAHETALALLDVPAYLQLKMNLGEGTGAALGMSVINATLHMLNDMKTFGEAEVAVA 335
                                    10        20        30        40        50        60        70|       86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326         
                                                                                                70|                                                                                                                                                                                                                                                                  
                                                                                                 77                                                                                                                                                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4hdrc_ C: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......eeeeeeeee.hhhhhhh......hhhhhhhhhhhh...hhhhhhhhhh..eeeeeeee...........ee................hhhhhhhhhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhh.hhhh.ee......hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hdr C   2 SLLQATVAKIMRPDTVIKDQVKTKLAGVLQSAGSLGRLEDMVEQYAGITGELNPALPKPCMVVASADHGVARRVVSAYPIETTIHMTANYLISQGASANAFANFCGADMVVVDMGVAGDLSYVPGLWHRKIAYGTQDFTEGPAMTREQAIQAVETGIDIVNDRVKHGNRCFCLGEMGIGNTTSSATIVGAFTGLAPEKVTGRGLKTKMEIVGRALAVNKPNPQDGLDVLAKVGGFELGALAGVILGSAANRCAVVIDGLNTTAAALIANVIHPLSKEYMFASHLSGEPAHSIALRQLQLEACLELGVRLGEGIGASMVVDMLYVAIKLLNN 339
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201  ||   218       228       238       248       258       268       278       288       298       308       318       328       338 
                                                                                                                                                                                                                                    204|                                                                                                                               
                                                                                                                                                                                                                                     212                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4hdrd_ D: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh........eeeeeeee.......hhhhhhhhhhh..hhhhhhhhhhheeeeeeeee..........eee................hhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hdr D   1 MLEELIAAIKPLDSIAMEQCQRRVDNLTKPLNSLHSFEHIACKLAGISGNPRPRALEKSIIIMAADNGVAQMTTAARLTGFCQGQAPIQVFAAHVQARLIMVDIGVAADLPHSPAVCRKKLAYGSRNSTEGPAMTRQQAIQAIEVGVRIAQAEIARGCQVIGLGEMGLGGLAAAMAIVACCHGQPLPGLAGREAELVNTAIAVNRPNAADPLDILTKVGGLAIAGLVGVILGAAAGRAAVVLDGLATSTAALIAINLVPDVKPYLIGSHFAAEPAHETALALLDVPAYLQLKMNLGEGTGAALGMSVINATLHMLNDMKTFGEAEVAV 334
                                    10        20        30        40        50        60        70|       86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        
                                                                                                70|                                                                                                                                                                                                                                                                 
                                                                                                 77
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 9)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        F6MZ55_9FIRM | F6MZ55: 4hdk 4hdm 4hdn 4hds
        F6MZ56_9FIRM | F6MZ56: 4hdk 4hdm 4hdn 4hds

(-) Related Entries Specified in the PDB File

4hdk SAME PROTEIN IN COMPLEX WITH PHLOROGLUCINOL.
4hdm SAME PROTEIN IN COMPLEX WITH P-CRESOL.
4hdn SAME PROTEIN IN SUBSTRATE-FREE STATE.
4hds