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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE (BDI_2101) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.91 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  30 Mar 10  (Deposition) - 02 Jun 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (Bdi_2101) From Parabacteroides Distasonis Atcc 8503 At 1. 91 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Vector Type: PLASMID
    Gene: BDI_2101
    Organism Scientific: PARABACTEROIDES DISTASONIS
    Organism Taxid: 435591
    Strain: ATCC 8503 / DSM 20701 / NCTC 11152

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 57)

Asymmetric/Biological Unit (9, 57)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA7Ligand/IonCALCIUM ION
3CAC1Ligand/IonCACODYLATE ION
4CL4Ligand/IonCHLORIDE ION
5MSE24Mod. Amino AcidSELENOMETHIONINE
6P6G1Ligand/IonHEXAETHYLENE GLYCOL
7PEG11Ligand/IonDI(HYDROXYETHYL)ETHER
8PG42Ligand/IonTETRAETHYLENE GLYCOL
9PGE5Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:322 , HOH A:579 , HOH A:580 , HOH A:581 , HOH A:582 , HOH A:583 , HOH A:584BINDING SITE FOR RESIDUE CA A 389
02AC2SOFTWAREASP A:55 , HOH A:519 , HOH A:552 , GLU B:146 , HOH B:617BINDING SITE FOR RESIDUE CA A 390
03AC3SOFTWAREASP A:55 , ASP A:91 , PGE A:403 , HOH A:621 , HOH A:630 , HOH B:593BINDING SITE FOR RESIDUE CA A 391
04AC4SOFTWAREGLU A:146 , HOH A:566 , HOH A:595 , ASP B:55 , ACT B:395 , HOH B:595BINDING SITE FOR RESIDUE CA A 392
05AC5SOFTWARELYS A:111 , GLY A:151BINDING SITE FOR RESIDUE CL A 393
06AC6SOFTWAREASN A:335 , HOH A:451 , HOH A:606 , HOH A:629BINDING SITE FOR RESIDUE CL A 394
07AC7SOFTWARESER A:105 , ILE A:107 , GLY A:144 , GLY A:145 , GLU A:146 , THR A:147 , HOH A:490 , HOH A:645BINDING SITE FOR RESIDUE ACT A 395
08AC8SOFTWAREILE A:29 , PHE A:30 , LYS A:176 , HOH A:468 , HOH A:558 , THR B:387BINDING SITE FOR RESIDUE PEG A 396
09AC9SOFTWAREGLN A:320 , ASP A:326 , TRP A:327 , SER A:328 , PHE A:386BINDING SITE FOR RESIDUE PEG A 397
10BC1SOFTWAREGLU A:300 , ASN A:301 , LYS A:374 , ASN A:375 , GLY B:43 , GLY B:44 , PRO B:46BINDING SITE FOR RESIDUE PEG A 398
11BC2SOFTWAREGLY A:181 , VAL A:369 , PGE A:402 , HOH A:435BINDING SITE FOR RESIDUE PEG A 399
12BC3SOFTWARELYS A:243BINDING SITE FOR RESIDUE PEG A 400
13BC4SOFTWARESER A:170 , VAL A:172 , ILE A:173 , ARG A:278 , ILE A:281 , HOH A:415 , HOH A:418 , HOH A:425 , HOH A:596BINDING SITE FOR RESIDUE PEG A 401
14BC5SOFTWAREPHE A:368 , PEG A:399 , HOH A:574 , SER B:217 , GLY B:240 , HOH B:463BINDING SITE FOR RESIDUE PGE A 402
15BC6SOFTWAREPHE A:34 , HIS A:53 , ASP A:91 , LYS A:294 , HIS A:297 , CA A:391 , HOH B:593BINDING SITE FOR RESIDUE PGE A 403
16BC7SOFTWARETHR A:209 , SER A:210 , HIS A:213 , ASP A:214 , SER A:323 , THR A:325 , HOH A:438 , HOH A:485 , HOH A:561 , HOH B:425BINDING SITE FOR RESIDUE P6G A 404
17BC8SOFTWAREHOH A:588 , ASP B:55 , ASP B:91 , ACT B:395 , HOH B:522 , HOH B:564 , HOH B:616BINDING SITE FOR RESIDUE CA B 389
18BC9SOFTWAREGLN B:322 , CAC B:394 , HOH B:582 , HOH B:583 , HOH B:584 , HOH B:585 , HOH B:586BINDING SITE FOR RESIDUE CA B 390
19CC1SOFTWAREGLY B:145 , HOH B:447 , HOH B:448 , HOH B:449 , HOH B:450 , HOH B:459BINDING SITE FOR RESIDUE CA B 391
20CC2SOFTWARELYS B:111 , ASP B:149 , VAL B:150 , GLY B:151 , HOH B:485 , HOH B:598BINDING SITE FOR RESIDUE CL B 392
21CC3SOFTWAREMSE B:203 , ASN B:335BINDING SITE FOR RESIDUE CL B 393
22CC4SOFTWAREARG A:303 , ARG A:385 , ASP B:214 , SER B:239 , GLN B:322 , SER B:323 , CA B:390BINDING SITE FOR RESIDUE CAC B 394
23CC5SOFTWARECA A:392 , ASP B:55 , MSE B:87 , ASN B:206 , SER B:288 , GLY B:289 , CA B:389 , HOH B:522 , HOH B:616BINDING SITE FOR RESIDUE ACT B 395
24CC6SOFTWARETHR B:209 , HIS B:213 , ASP B:214 , VAL B:232BINDING SITE FOR RESIDUE PEG B 396
25CC7SOFTWAREASP B:40 , ILE B:41 , PRO B:46 , HOH B:423BINDING SITE FOR RESIDUE PEG B 397
26CC8SOFTWARETYR B:195BINDING SITE FOR RESIDUE PEG B 398
27CC9SOFTWARETHR A:71 , LYS B:276BINDING SITE FOR RESIDUE PEG B 399
28DC1SOFTWAREASN A:177 , GLN A:179 , ARG B:385 , THR B:387BINDING SITE FOR RESIDUE PEG B 400
29DC2SOFTWAREMSE A:136 , THR A:194 , SER A:358 , PHE A:359 , LYS B:111BINDING SITE FOR RESIDUE PGE B 401
30DC3SOFTWAREPHE B:34 , HIS B:53 , ASP B:91 , GLY B:289 , LYS B:294 , HIS B:297BINDING SITE FOR RESIDUE PGE B 402
31DC4SOFTWARELEU B:242 , GLU B:321 , GLN B:322BINDING SITE FOR RESIDUE PGE B 403
32DC5SOFTWAREGLU B:70 , TYR B:219 , LYS B:243BINDING SITE FOR RESIDUE PG4 B 404
33DC6SOFTWAREGLU A:132 , THR A:194 , LYS B:69 , LYS B:111 , LEU B:112 , HOH B:484BINDING SITE FOR RESIDUE PG4 B 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MDO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MDO)

(-) 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:365
 aligned with A6LDR8_PARD8 | A6LDR8 from UniProtKB/TrEMBL  Length:388

    Alignment length:365
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383     
         A6LDR8_PARD8    24 NIDKGIFPKAFCKIIPDILGGDPEYCNIMHADGAGTKSSLAYMYWKETGDLSVWKGIAQDALIMNIDDLLCVGAVDNILVSSTIGRNKLLVPGEVISAIINGTDELLAELREMGVGCYATGGETADVGDLVRTIIVDSTVTCRMKRSDVIDNKNIQGGDVIVGLASSGQATYEKEYNGGMGSNGLTSARHDVFSKYLAKKYPESYDAAVPKELVYSGGLKLTDKIEELGIDAGKMVLSPTRTYAPVIKVLLDKLRSQIHGMVHCSGGAQTKVMHFVENKRVTKDNLFPIPPLFRTIQEQSGTDWSEMYKVFNMGHRMEIYIAPEHAEEVIGISKSFGIDAQIVGFVEEADKNELIIESEKGRFTY 388
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee........eeeeeeeee..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.......eeeeeeeeeeee.hhh.hhhhh....eeeeee..................hhhhhhhhhh.hhhhhhhhhhh..................ee....eehhhhhhh....hhhhhhhhhhhhhhhh.eeee...hhhhhhhhhh..eeeee......hhhhhhhhhhhh.hhhhhhhhh...eeeeeeehhhhhhhhhhhhhhh...eeeeeeeee....eeeeee..eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mdo A  24 NIDKGIFPKAFCKIIPDILGGDPEYCNImHADGAGTKSSLAYmYWKETGDLSVWKGIAQDALImNIDDLLCVGAVDNILVSSTIGRNKLLVPGEVISAIINGTDELLAELREmGVGCYATGGETADVGDLVRTIIVDSTVTCRmKRSDVIDNKNIQGGDVIVGLASSGQATYEKEYNGGmGSNGLTSARHDVFSKYLAKKYPESYDAAVPKELVYSGGLKLTDKIEELGIDAGKmVLSPTRTYAPVIKVLLDKLRSQIHGmVHCSGGAQTKVmHFVENKRVTKDNLFPIPPLFRTIQEQSGTDWSEmYKVFNmGHRmEIYIAPEHAEEVIGISKSFGIDAQIVGFVEEADKNELIIESEKGRFTY 388
                                    33        43        53        63  |     73        83   |    93       103       113       123       133  |    143       153       163   |   173       183       193       203       213       223       233       243       253    |  263       273       283|      293  |    303       313       323      |333  |   |343       353       363       373       383     
                                                       52-MSE        66-MSE               87-MSE                                          136-MSE                        167-MSE                             203-MSE                                                258-MSE                   284-MSE     296-MSE                           330-MSE |   |                                                
                                                                                                                                                                                                                                                                                                                                                  336-MSE                                                
                                                                                                                                                                                                                                                                                                                                                      340-MSE                                            


Chain B from PDB  Type:PROTEIN  Length:363
 aligned with A6LDR8_PARD8 | A6LDR8 from UniProtKB/TrEMBL  Length:388

    Alignment length:363
                                    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       365       375       385   
         A6LDR8_PARD8    26 DKGIFPKAFCKIIPDILGGDPEYCNIMHADGAGTKSSLAYMYWKETGDLSVWKGIAQDALIMNIDDLLCVGAVDNILVSSTIGRNKLLVPGEVISAIINGTDELLAELREMGVGCYATGGETADVGDLVRTIIVDSTVTCRMKRSDVIDNKNIQGGDVIVGLASSGQATYEKEYNGGMGSNGLTSARHDVFSKYLAKKYPESYDAAVPKELVYSGGLKLTDKIEELGIDAGKMVLSPTRTYAPVIKVLLDKLRSQIHGMVHCSGGAQTKVMHFVENKRVTKDNLFPIPPLFRTIQEQSGTDWSEMYKVFNMGHRMEIYIAPEHAEEVIGISKSFGIDAQIVGFVEEADKNELIIESEKGRFTY 388
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------AIRS_C-3mdoB01 B:179-380                                                                                                                                                                                  -------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------AIRS_C-3mdoB02 B:179-380                                                                                                                                                                                  -------- Pfam domains (2)
         Sec.struct. author ............ee........eeeeeeeee..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.......eeeeeeeeeeee.hhh.hhhhh....eeeeee..................hhhhhhhh...hhhhhhhhhhh....hhhhh................hhhhhhh.....hhhhhhhhhhhhh..eeeeee...hhhhhhhhh...eeeee......hhhhhhhhhhhh.hhhhhhhhh...eeeeeee...hhhhhhhhhhh....eeeeeeeee....eeeeee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mdo B  26 DKGIFPKAFCKIIPDILGGDPEYCNImHADGAGTKSSLAYmYWKETGDLSVWKGIAQDALImNIDDLLCVGAVDNILVSSTIGRNKLLVPGEVISAIINGTDELLAELREmGVGCYATGGETADVGDLVRTIIVDSTVTCRmKRSDVIDNKNIQGGDVIVGLASSGQATYEKEYNGGmGSNGLTSARHDVFSKYLAKKYPESYDAAVPKELVYSGGLKLTDKIEELGIDAGKmVLSPTRTYAPVIKVLLDKLRSQIHGmVHCSGGAQTKVmHFVENKRVTKDNLFPIPPLFRTIQEQSGTDWSEmYKVFNmGHRmEIYIAPEHAEEVIGISKSFGIDAQIVGFVEEADKNELIIESEKGRFTY 388
                                    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       365       375       385   
                                                     52-MSE        66-MSE               87-MSE                                          136-MSE                        167-MSE                             203-MSE                                                258-MSE                   284-MSE     296-MSE                           330-MSE |   |                                                
                                                                                                                                                                                                                                                                                                                                                336-MSE                                                
                                                                                                                                                                                                                                                                                                                                                    340-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3MDO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MDO)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: AIRS_C] (13)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A6LDR8_PARD8 | A6LDR8)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.

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