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(-) Description

Title :  RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS
 
Authors :  T. N. Petersen, S. Kauppinen, S. Larsen
Date :  26 Feb 97  (Deposition) - 04 Mar 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Inverting, Parallel Beta-Helix, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. N. Petersen, S. Kauppinen, S. Larsen
The Crystal Structure Of Rhamnogalacturonase A From Aspergillus Aculeatus: A Right-Handed Parallel Beta Helix.
Structure V. 5 533 1997
PubMed-ID: 9115442  |  Reference-DOI: 10.1016/S0969-2126(97)00209-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHAMNOGALACTURONASE A
    Chains: A
    EC Number: 3.2.1.-
    Engineered: YES
    Expression System: ASPERGILLUS ORYZAE
    Expression System Taxid: 5062
    Organism Scientific: ASPERGILLUS ACULEATUS
    Organism Taxid: 5053
    Synonym: RGASE A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric/Biological Unit (4, 26)
No.NameCountTypeFull Name
1BMA6Ligand/IonBETA-D-MANNOSE
2GLC1Ligand/IonALPHA-D-GLUCOSE
3MAN15Ligand/IonALPHA-D-MANNOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:32 , ASN A:59 , TYR A:83 , PHE A:115 , NAG A:424 , MAN A:437 , HOH A:527 , HOH A:605BINDING SITE FOR RESIDUE NAG A 423
02AC2SOFTWAREPHE A:115 , TYR A:117 , NAG A:423 , MAN A:437 , BMA A:442BINDING SITE FOR RESIDUE NAG A 424
03AC3SOFTWARENAG A:424 , BMA A:439 , BMA A:441 , MAN A:445BINDING SITE FOR RESIDUE BMA A 442
04AC4SOFTWAREBMA A:442BINDING SITE FOR RESIDUE MAN A 445
05AC5SOFTWAREBMA A:442BINDING SITE FOR RESIDUE BMA A 441
06AC6SOFTWAREASN A:263 , VAL A:264 , ASN A:299 , NAG A:443 , HOH A:549 , HOH A:608BINDING SITE FOR RESIDUE NAG A 425
07AC7SOFTWAREGLN A:1 , NAG A:425 , BMA A:446BINDING SITE FOR RESIDUE NAG A 443
08AC8SOFTWARENAG A:443BINDING SITE FOR RESIDUE BMA A 446
09AC9SOFTWARESER A:368 , BMA A:427 , MAN A:447BINDING SITE FOR RESIDUE MAN A 426
10BC1SOFTWAREASP A:324 , ARG A:351 , SER A:368 , TYR A:369 , THR A:370 , MAN A:426BINDING SITE FOR RESIDUE BMA A 427
11BC2SOFTWAREGLN A:77 , THR A:385 , MAN A:436 , MAN A:444 , HOH A:554 , HOH A:602BINDING SITE FOR RESIDUE MAN A 428
12BC3SOFTWAREASN A:311 , THR A:398BINDING SITE FOR RESIDUE MAN A 429
13BC4SOFTWARETYR A:54 , SER A:409 , TYR A:411 , PRO A:412 , GLY A:413 , LEU A:414 , MAN A:438 , HOH A:491 , HOH A:505 , HOH A:524 , HOH A:557 , HOH A:621BINDING SITE FOR RESIDUE MAN A 430
14BC5SOFTWAREGLU A:162 , SER A:418 , HOH A:604BINDING SITE FOR RESIDUE MAN A 431
15BC6SOFTWARETHR A:372 , THR A:374 , MAN A:440BINDING SITE FOR RESIDUE MAN A 432
16BC7SOFTWARETHR A:405 , PRO A:407 , HOH A:550BINDING SITE FOR RESIDUE GLC A 433
17BC8SOFTWARESER A:373 , THR A:374BINDING SITE FOR RESIDUE MAN A 434
18BC9SOFTWARETHR A:372 , MAN A:440BINDING SITE FOR RESIDUE BMA A 435
19CC1SOFTWARESER A:383 , THR A:385 , MAN A:428BINDING SITE FOR RESIDUE MAN A 436
20CC2SOFTWARESER A:400 , PRO A:402 , NAG A:423 , NAG A:424 , HOH A:465 , HOH A:541BINDING SITE FOR RESIDUE MAN A 437
21CC3SOFTWARELEU A:24 , THR A:408 , MAN A:430 , HOH A:557 , HOH A:621 , HOH A:625BINDING SITE FOR RESIDUE MAN A 438
22CC4SOFTWARETHR A:376 , BMA A:442BINDING SITE FOR RESIDUE BMA A 439
23CC5SOFTWARETHR A:371 , MAN A:432 , BMA A:435BINDING SITE FOR RESIDUE MAN A 440
24CC6SOFTWARETHR A:386 , MET A:387 , MAN A:428 , HOH A:623BINDING SITE FOR RESIDUE MAN A 444
25CC7SOFTWARELYS A:361 , THR A:367 , SER A:368 , MAN A:426BINDING SITE FOR RESIDUE MAN A 447
26CC8SOFTWAREASP A:31 , SER A:380BINDING SITE FOR RESIDUE MAN A 448

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:21 -A:47
2A:199 -A:216
3A:322 -A:328
4A:350 -A:359

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:204 -Pro A:205
2Gly A:225 -Ser A:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RMG)

(-) Exons   (0, 0)

(no "Exon" information available for 1RMG)

(-) 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:422
 aligned with RHGA_ASPAC | Q00001 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:422
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438  
           RHGA_ASPAC    19 QLSGSVGPLTSASTKGATKTCNILSYGAVADNSTDVGPAITSAWAACKSGGLVYIPSGNYALNTWVTLTGGSATAIQLDGIIYRTGTASGNMIAVTDTTDFELFSSTSKGAVQGFGYVYHAEGTYGARILRLTDVTHFSVHDVILVDAPAFHFTMDTCSDGEVYNMAIRGGNEGGLDGIDVWGSNIWVHDVEVTNKDECVTVKSPANNILVESIYCNWSGGCAMGSLGADTDVTDIVYRNVYTWSSNQMYMIKSNGGSGTVSNVLLENFIGHGNAYSLDIDGYWSSMTAVAGDGVQLNNITVKNWKGTEANGATRPPIRVVCSDTAPCTDLTLEDIAIWTESGSSELYLCRSAYGSGYCLKDSSSHTSYTTTSTVTAAPSGYSATTMAADLATAFGLTASIPIPTIPTSFYPGLTPYSALAG 440
               SCOP domains d1rmga_ A: Rhamnogalacturonase A                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1rmgA00 A:1-422 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------Glyco_hydro_28-1rmgA01 A:47-359                                                                                                                                                                                                                                                                                          --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhheee.............hhhhhhhhhhhhh..eeeee..eeeee...eeee.ee.eeeeeeeeeee........eeee.ee.eeeee....eeee..hhhhhhh.......eeee.ee.eeee.eeee......eeee.ee.eeee.eeeeee.......eeeeee.eeee.eeee.....eeee.eee.eeee.eeee....eee......eeee.eee..eeee.....eeeeee....eee.eeee.eeee.....eeee..............eee.eeee.eeeee........eeeee.....ee.eeee.eeeee.......eee..eeee............eeeeeee............................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rmg A   1 QLSGSVGPLTSASTKGATKTCNILSYGAVADNSTDVGPAITSAWAACKSGGLVYIPSGNYALNTWVTLTGGSATAIQLDGIIYRTGTASGNMIAVTDTTDFELFSSTSKGAVQGFGYVYHAEGTYGARILRLTDVTHFSVHDIILVDAPAFHFTMDTCSDGEVYNMAIRGGNEGGLDGIDVWGSNIWVHDVEVTNKDECVTVKSPANNILVESIYCNWSGGCAMGSLGADTDVTDIVYRNVYTWSSNQMYMIKSNGGSGTVSNVLLENFIGHGNAYSLDIDGYWSSMTAVAGDGVQLNNITVKNWKGTEANGATRPPIRVVCSDTAPCTDLTLEDIAIWTESGSSELYLCRSAYGSGYCLKDSSSHTSYTTTSTVTAAPSGYSATTMAADLATAFGLTASIPIPTIPTSFYPGLTPYSALAG 422
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Pec_lyase (42)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RHGA_ASPAC | Q00001)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004650    polygalacturonase activity    Catalysis of the random hydrolysis of (1->4)-alpha-D-galactosiduronic linkages in pectate and other galacturonans.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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