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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE ASPARAGINYL HYDROXYLASE (2636534) FROM BACILLUS SUBTILIS AT 2.60 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  18 Feb 05  (Deposition) - 15 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  2636534, Putative Asparaginyl Hydroxylase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Asparaginyl Hydroxylase (2636534) From Bacillus Subtilis At 2. 60 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE ASPARAGINYL HYDROXYLASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YXBC
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 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, 24)

Asymmetric Unit (2, 24)
No.NameCountTypeFull Name
1FE4Ligand/IonFE (III) ION
2MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:145 , ASP A:147 , HIS A:224 , HOH A:561BINDING SITE FOR RESIDUE FE A 555
2AC2SOFTWAREHIS B:145 , ASP B:147 , HIS B:224BINDING SITE FOR RESIDUE FE B 555
3AC3SOFTWAREHIS C:145 , ASP C:147 , HIS C:224BINDING SITE FOR RESIDUE FE C 555
4AC4SOFTWAREHIS D:145 , ASP D:147 , HIS D:224 , HOH D:561 , HOH D:562BINDING SITE FOR RESIDUE FE D 555

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Ser A:14 -Pro A:15
2Trp A:26 -Pro A:27
3Asn A:138 -Gly A:139
4Ser B:14 -Pro B:15
5Trp B:26 -Pro B:27
6Trp C:26 -Pro C:27
7Ser D:14 -Pro D:15
8Trp D:26 -Pro D:27
9Asn D:138 -Gly D:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.YXBC_BACSU96-256
 
 
 		  4A:96-256
B:96-256
C:97-256
D:96-256
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.YXBC_BACSU96-256
 
 
 		  2A:96-256
B:96-256
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.YXBC_BACSU96-256
 
 
 		  2-
-
C:97-256
D:96-256

(-) Exons   (0, 0)

(no "Exon" information available for 1VRB)

(-) 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:302
 aligned with YXBC_BACSU | P46327 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:319
                                    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         
           YXBC_BACSU     8 VLESIISPVTMSEFLEEYWPVKPLVARGEVERFTSIPGFEKVRTLENVLAIYNNPVMVVGDAVIEESEGITDRFLVSPAEALEWYEKGAALEFDFTDLFIPQVRRWIEKLKAELRLPAGTSSKAIVYAAKNGGGFKAHFDAYTNLIFQIQGEKTWKLAKNENVSNPMQHYDLSEAPYYPDDLQSYWKGDPPKEDLPDAEIVNLTPGTMLYLPRGLWHSTKSDQATLALNITFGQPAWLDLMLAALRKKLISDNRFRELAVNHQSLHESSKSELNGYLESLIQTLSENAETLTPEQIFQSQDSDFDPYQSTQLVFRQLLT 326
               SCOP domains d1vrba1 A:8-326 Putative asparaginyl hydroxylase YxbC                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..hhhhhhhhh.....eee..hhhhhhhh..hhhhhhhhhhhhhh...eee.-------------.eeehhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhh.......eeeeeeee........ee...eeeeeeee..eeeeee...........ee..----.hhhhhhhh............eeeee....eeee....eeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------JMJC  PDB: A:96-256 UniProt: 96-256                                                                                                                              ---------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vrb A   8 VLESIISPVTmSEFLEEYWPVKPLVARGEVERFTSIPGFEKVRTLENVLAIYNNPVmVV-------------RFLVSPAEALEWYEKGAALEFDFTDLFIPQVRRWIEKLKAELRLPAGTSSKAIVYAAKNGGGFKAHFDAYTNLIFQIQGEKTWKLAKNENVSNPmQHYDLS----YPDDLQSYWKGDPPKEDLPDAEIVNLTPGTmLYLPRGLWHSTKSDQATLALNITFGQPAWLDLmLAALRKKLISDNRFRELAVNHQSLHESSKSELNGYLESLIQTLSENAETLTPEQIFQSQDSDFDPYQSTQLVFRQLLT 326
                                    17|       27        37        47        57      | |-         -  |     87        97       107       117       127       137       147       157       167      |177  |    187       197       207       217       227       237       247|      257       267       277       287       297       307       317         
                                     18-MSE                                        64-MSE          80                                                                                           174-MSE80  185                           215-MSE                          248-MSE                                                                          
                                                                                     66                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:311
 aligned with YXBC_BACSU | P46327 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:319
                                    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         
           YXBC_BACSU     8 VLESIISPVTMSEFLEEYWPVKPLVARGEVERFTSIPGFEKVRTLENVLAIYNNPVMVVGDAVIEESEGITDRFLVSPAEALEWYEKGAALEFDFTDLFIPQVRRWIEKLKAELRLPAGTSSKAIVYAAKNGGGFKAHFDAYTNLIFQIQGEKTWKLAKNENVSNPMQHYDLSEAPYYPDDLQSYWKGDPPKEDLPDAEIVNLTPGTMLYLPRGLWHSTKSDQATLALNITFGQPAWLDLMLAALRKKLISDNRFRELAVNHQSLHESSKSELNGYLESLIQTLSENAETLTPEQIFQSQDSDFDPYQSTQLVFRQLLT 326
               SCOP domains d1vrbb_ B: Putative asparaginyl hydroxylase YxbC                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...hhhhhhhh.....eee..hhhhhhhh.hhhhhhhhhhhhhhh...eeeehhhhhh....---.eee...hhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeee...eeeeeeee..eeeeee...........ee.-----...hhhhh.............eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------JMJC  PDB: B:96-256 UniProt: 96-256                                                                                                                              ---------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vrb B   8 VLESIISPVTmSEFLEEYWPVKPLVARGEVERFTSIPGFEKVRTLENVLAIYNNPVmVVGDAVIEESEG---RFLVSPAEALEWYEKGAALEFDFTDLFIPQVRRWIEKLKAELRLPAGTSSKAIVYAAKNGGGFKAHFDAYTNLIFQIQGEKTWKLAKNENVSNPmQHYDL-----YPDDLQSYWKGDPPKEDLPDAEIVNLTPGTmLYLPRGLWHSTKSDQATLALNITFGQPAWLDLmLAALRKKLISDNRFRELAVNHQSLHESSKSELNGYLESLIQTLSENAETLTPEQIFQSQDSDFDPYQSTQLVFRQLLT 326
                                    17|       27        37        47        57      | 67        |-  |     87        97       107       117       127       137       147       157       167      |177 |     187       197       207       217       227       237       247|      257       267       277       287       297       307       317         
                                     18-MSE                                        64-MSE      76  80                                                                                           174-MSE9   185                           215-MSE                          248-MSE                                                                          


Chain C from PDB  Type:PROTEIN  Length:298
 aligned with YXBC_BACSU | P46327 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:319
                                    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         
           YXBC_BACSU     8 VLESIISPVTMSEFLEEYWPVKPLVARGEVERFTSIPGFEKVRTLENVLAIYNNPVMVVGDAVIEESEGITDRFLVSPAEALEWYEKGAALEFDFTDLFIPQVRRWIEKLKAELRLPAGTSSKAIVYAAKNGGGFKAHFDAYTNLIFQIQGEKTWKLAKNENVSNPMQHYDLSEAPYYPDDLQSYWKGDPPKEDLPDAEIVNLTPGTMLYLPRGLWHSTKSDQATLALNITFGQPAWLDLMLAALRKKLISDNRFRELAVNHQSLHESSKSELNGYLESLIQTLSENAETLTPEQIFQSQDSDFDPYQSTQLVFRQLLT 326
               SCOP domains d1vrbc_ C: Putative asparaginyl hydroxylase YxbC                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...hhhhhhhh.....eee..hhhhhhhh.hhhhhhhhhhhhhhh...ee..-------------..ee.hhhhhhhhh---.eee.hhhhhhhhhhhhhhhhhhhh.......eeeeeee...-..eeeee...eeeeeeee..eeeeee...........ee..----.hhhhhh..............eeeee....eeee....eeeee.....eeeeeee...hhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------JMJC  PDB: C:97-256 UniProt: 96-256                                                                                                                              ---------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vrb C   8 VLESIISPVTmSEFLEEYWPVKPLVARGEVERFTSIPGFEKVRTLENVLAIYNNPVmVV-------------RFLVSPAEALEWYE---ALEFDFTDLFIPQVRRWIEKLKAELRLPAGTSSKAIVYAAKN-GGFKAHFDAYTNLIFQIQGEKTWKLAKNENVSNPmQHYDLS----YPDDLQSYWKGDPPKEDLPDAEIVNLTPGTmLYLPRGLWHSTKSDQATLALNITFGQPAWLDLmLAALRKKLISDNRFRELAVNHQSLHESSKSELNGYLESLIQTLSENAETLTPEQIFQSQDSDFDPYQSTQLVFRQLLT 326
                                    17|       27        37        47        57      | |-         -  |     87     |  97       107       117       127       137| |    147       157       167      |177  |    187       197       207       217       227       237       247|      257       267       277       287       297       307       317         
                                     18-MSE                                        64-MSE          80           93  97                                      138 |                               174-MSE80  185                           215-MSE                          248-MSE                                                                          
                                                                                     66                                                                       140                                                                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:313
 aligned with YXBC_BACSU | P46327 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:320
                                    16        26        36        46        56        66        76        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
           YXBC_BACSU     7 SVLESIISPVTMSEFLEEYWPVKPLVARGEVERFTSIPGFEKVRTLENVLAIYNNPVMVVGDAVIEESEGITDRFLVSPAEALEWYEKGAALEFDFTDLFIPQVRRWIEKLKAELRLPAGTSSKAIVYAAKNGGGFKAHFDAYTNLIFQIQGEKTWKLAKNENVSNPMQHYDLSEAPYYPDDLQSYWKGDPPKEDLPDAEIVNLTPGTMLYLPRGLWHSTKSDQATLALNITFGQPAWLDLMLAALRKKLISDNRFRELAVNHQSLHESSKSELNGYLESLIQTLSENAETLTPEQIFQSQDSDFDPYQSTQLVFRQLLT 326
               SCOP domains d1vrbd_ D: Putative asparaginyl hydroxylase YxbC                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------Cupin_4-1vrbD01 D:18-326                                                                                                                                                                                                                                                                                              Pfam domains (1)
           Pfam domains (2) -----------Cupin_4-1vrbD02 D:18-326                                                                                                                                                                                                                                                                                              Pfam domains (2)
           Pfam domains (3) -----------Cupin_4-1vrbD03 D:18-326                                                                                                                                                                                                                                                                                              Pfam domains (3)
           Pfam domains (4) -----------Cupin_4-1vrbD04 D:18-326                                                                                                                                                                                                                                                                                              Pfam domains (4)
         Sec.struct. author ..hhhhhh..hhhhhhhhh.....eee..hhhhhhhh..hhhhhhhhhhhhhh...eeeehhhhhhhh----.eeeehhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeeee........ee...eeeeeeee..eeeeee...........ee.......hhhhhh..............eeeee....eeee....eeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhh.......---hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------JMJC  PDB: D:96-256 UniProt: 96-256                                                                                                                              ---------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vrb D   7 SVLESIISPVTmSEFLEEYWPVKPLVARGEVERFTSIPGFEKVRTLENVLAIYNNPVmVVGDAVIEES----DRFLVSPAEALEWYEKGAALEFDFTDLFIPQVRRWIEKLKAELRLPAGTSSKAIVYAAKNGGGFKAHFDAYTNLIFQIQGEKTWKLAKNENVSNPmQHYDLSEAPYYPDDLQSYWKGDPPKEDLPDAEIVNLTPGTmLYLPRGLWHSTKSDQATLALNITFGQPAWLDLmLAALRKKLISDNRFRELAVNHQ---ESSKSELNGYLESLIQTLSENAETLTPEQIFQSQDSDFDPYQSTQLVFRQLLT 326
                                    16 |      26        36        46        56       |66       | -  |     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
                                      18-MSE                                        64-MSE    74   79                                                                                            174-MSE                                  215-MSE                          248-MSE               270 274
   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: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VRB)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (YXBC_BACSU | P46327)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  1vrb
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