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(-) Description

Title :  CRYSTAL STRUCTURE OF RUMINOCOCCUS ALBUS BETA-(1,4)-MANNOOLIGOSACCHARIDE PHOSPHORYLASE (RAMP2) IN COMPLEXES WITH PHOSPHATE
 
Authors :  Y. Ye, W. Saburi, K. Kato, M. Yao
Date :  13 Aug 15  (Deposition) - 23 Mar 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Glycoside Hydrolase Family 130, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Ye, W. Saburi, R. Odaka, K. Kato, N. Sakurai, K. Komoda, M. Nishimoto M. Kitaoka, H. Mori, M. Yao
Structural Insights Into The Difference In Substrate Recognition Of Two Mannoside Phosphorylases From Two Gh130 Subfamilies.
Febs Lett. V. 590 828 2016
PubMed-ID: 26913570  |  Reference-DOI: 10.1002/1873-3468.12105

(-) Compounds

Molecule 1 - BETA-1,4-MANNOOLIGOSACCHARIDE PHOSPHORYLASE
    Chains: A, B, C, D, E, F
    EC Number: 2.4.1.319
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-335
    Gene: RUMAL_0099
    Organism Scientific: RUMINOCOCCUS ALBUS (STRAIN ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7)
    Organism Taxid: 697329
    Strain: ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7
    Synonym: RAMP2

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1PO46Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:162 , ASN A:163 , ARG A:180 , LYS A:220 , HIS A:239 , TYR A:250 , HOH A:647binding site for residue PO4 A 401
2AC2SOFTWAREARG B:162 , ASN B:163 , ARG B:180 , LYS B:220 , HIS B:239 , TYR B:250 , HOH B:512binding site for residue PO4 B 401
3AC3SOFTWAREARG C:162 , ASN C:163 , ARG C:180 , LYS C:220 , HIS C:239 , TYR C:250 , HOH C:621 , HOH C:661binding site for residue PO4 C 401
4AC4SOFTWAREARG D:162 , ASN D:163 , ARG D:180 , LYS D:220 , HIS D:239 , TYR D:250 , HOH D:630binding site for residue PO4 D 401
5AC5SOFTWAREARG E:162 , ASN E:163 , ARG E:180 , LYS E:220 , HIS E:239 , TYR E:250 , HOH E:541binding site for residue PO4 E 401
6AC6SOFTWAREARG F:162 , ASN F:163 , ARG F:180 , LYS F:220 , HIS F:239 , TYR F:250 , HOH F:609binding site for residue PO4 F 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AYD)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Asn A:33 -Pro A:34
2Pro A:159 -Phe A:160
3Asn B:33 -Pro B:34
4Pro B:159 -Phe B:160
5Asn C:33 -Pro C:34
6Pro C:159 -Phe C:160
7Asn D:33 -Pro D:34
8Pro D:159 -Phe D:160
9Asn E:33 -Pro E:34
10Pro E:159 -Phe E:160
11Asn F:33 -Pro F:34
12Pro F:159 -Phe F:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AYD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AYD)

(-) Exons   (0, 0)

(no "Exon" information available for 5AYD)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................ee..............eeeeeeeeeeeeee..eeeeeeeeeee....eeeeeeee......ee.......ee.hhhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeee.....eee........eeeeee........eeeeeee..........eeeeee......eeeeeee...hhhhh.eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eeee.........hhhhhh......eeeeeeee.....eeeeeeee...eeeeeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ayd A   1 MKTQIINGVSLPNIPWQDKPADCKDVIWRYDANPIIPRDQLPTSNSIFNSAVVPYESEKGKFAGVFRVDDKCRNMELHAGFSKDGIHWDINPDRIVFEQAEKSTEEVNQWGYGYDPRVCFIEDRFWVTWCNAYGWKPTIGVAYTFDFKTFYQCENAFLPFNRNGVLFPRKINGKYVMFSRPSDSGHTPFGDMFISQSPDMKYWGEHRHVMGPLRAWESKKIGAGPIPIETSEGWLCFYHGVLESCNGFVYSFSACILDKDEPWKVKYRCAEYLLSPQKIYECVGDVQNVTFPCATLVDADTGRIAIYYGCADTCVSMAFTTVDDVVDYVKSHSSV 335
                                    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     


Chain B from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................ee..............eeeeeeeeeee.......eeeeeeeee....eeeeeeee.....eee.......ee.hhhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeee......ee........eeeeee........eeeeeee..........eeeeee......eeeeeee...hhhhh.eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eeee.........hhhhhh......eeeeeeee.....eeeeeeee...eeeeeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ayd B   1 MKTQIINGVSLPNIPWQDKPADCKDVIWRYDANPIIPRDQLPTSNSIFNSAVVPYESEKGKFAGVFRVDDKCRNMELHAGFSKDGIHWDINPDRIVFEQAEKSTEEVNQWGYGYDPRVCFIEDRFWVTWCNAYGWKPTIGVAYTFDFKTFYQCENAFLPFNRNGVLFPRKINGKYVMFSRPSDSGHTPFGDMFISQSPDMKYWGEHRHVMGPLRAWESKKIGAGPIPIETSEGWLCFYHGVLESCNGFVYSFSACILDKDEPWKVKYRCAEYLLSPQKIYECVGDVQNVTFPCATLVDADTGRIAIYYGCADTCVSMAFTTVDDVVDYVKSHSSV 335
                                    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     


Chain C from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................ee..............eeeeeeeeeeeeee..eeeeeeeeeee....eeeeeeee......ee.......ee.hhhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeee......ee........eeeeee........eeeeeee..........eeeeee......eeeeeee...hhhhh.eeee....eee..eeeeeeeeeee....eeeeeeeeee.......eeee.........hhhhhh......eeeeeeee.....eeeeeeee...eeeeeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ayd C   1 MKTQIINGVSLPNIPWQDKPADCKDVIWRYDANPIIPRDQLPTSNSIFNSAVVPYESEKGKFAGVFRVDDKCRNMELHAGFSKDGIHWDINPDRIVFEQAEKSTEEVNQWGYGYDPRVCFIEDRFWVTWCNAYGWKPTIGVAYTFDFKTFYQCENAFLPFNRNGVLFPRKINGKYVMFSRPSDSGHTPFGDMFISQSPDMKYWGEHRHVMGPLRAWESKKIGAGPIPIETSEGWLCFYHGVLESCNGFVYSFSACILDKDEPWKVKYRCAEYLLSPQKIYECVGDVQNVTFPCATLVDADTGRIAIYYGCADTCVSMAFTTVDDVVDYVKSHSSV 335
                                    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     


Chain D from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................ee..............eeeeeeeeeee.......eeeeeeeee....eeeeeeee......ee.......ee.hhhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeee......ee........eeeeee........eeeeeee..........eeeeee......eeeeeee...hhhhh.eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eeee.........hhhhhh......eeeeeeee.....eeeeeeee...eeeeeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ayd D   1 MKTQIINGVSLPNIPWQDKPADCKDVIWRYDANPIIPRDQLPTSNSIFNSAVVPYESEKGKFAGVFRVDDKCRNMELHAGFSKDGIHWDINPDRIVFEQAEKSTEEVNQWGYGYDPRVCFIEDRFWVTWCNAYGWKPTIGVAYTFDFKTFYQCENAFLPFNRNGVLFPRKINGKYVMFSRPSDSGHTPFGDMFISQSPDMKYWGEHRHVMGPLRAWESKKIGAGPIPIETSEGWLCFYHGVLESCNGFVYSFSACILDKDEPWKVKYRCAEYLLSPQKIYECVGDVQNVTFPCATLVDADTGRIAIYYGCADTCVSMAFTTVDDVVDYVKSHSSV 335
                                    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     


Chain E from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................ee..............eeeeeeeeeeeeee..eeeeeeeeeee....eeeeeeee......ee.......ee.hhhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeee......ee........eeeeee........eeeeeee..........eeeeee......eeeeeee...hhhhh.eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eeee.........hhhhhh......eeeeeeee.....eeeeeeee...eeeeeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ayd E   1 MKTQIINGVSLPNIPWQDKPADCKDVIWRYDANPIIPRDQLPTSNSIFNSAVVPYESEKGKFAGVFRVDDKCRNMELHAGFSKDGIHWDINPDRIVFEQAEKSTEEVNQWGYGYDPRVCFIEDRFWVTWCNAYGWKPTIGVAYTFDFKTFYQCENAFLPFNRNGVLFPRKINGKYVMFSRPSDSGHTPFGDMFISQSPDMKYWGEHRHVMGPLRAWESKKIGAGPIPIETSEGWLCFYHGVLESCNGFVYSFSACILDKDEPWKVKYRCAEYLLSPQKIYECVGDVQNVTFPCATLVDADTGRIAIYYGCADTCVSMAFTTVDDVVDYVKSHSSV 335
                                    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     


Chain F from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................ee..............eeeeeeeeeee.......eeeeeeeee....eeeeeeee......ee.......ee.hhhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeee......ee........eeeeee........eeeeeee..........eeeeee......eeeeeee...hhhhh.eeee....eee..eeeeeeeeeee....eeeeeeeeee.......eeee.........hhhhhh......eeeeeeee.....eeeeeeee...eeeeeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ayd F   1 MKTQIINGVSLPNIPWQDKPADCKDVIWRYDANPIIPRDQLPTSNSIFNSAVVPYESEKGKFAGVFRVDDKCRNMELHAGFSKDGIHWDINPDRIVFEQAEKSTEEVNQWGYGYDPRVCFIEDRFWVTWCNAYGWKPTIGVAYTFDFKTFYQCENAFLPFNRNGVLFPRKINGKYVMFSRPSDSGHTPFGDMFISQSPDMKYWGEHRHVMGPLRAWESKKIGAGPIPIETSEGWLCFYHGVLESCNGFVYSFSACILDKDEPWKVKYRCAEYLLSPQKIYECVGDVQNVTFPCATLVDADTGRIAIYYGCADTCVSMAFTTVDDVVDYVKSHSSV 335
                                    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
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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 5AYD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AYD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AYD)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  5ayd
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        MOSP_RUMA7 | E6UBR9: 5aye

(-) Related Entries Specified in the PDB File

5ay9 5ayc 5aye